Compare commits
1 Commits
pip-standa
...
abandoned_
| Author | SHA1 | Date | |
|---|---|---|---|
| 1a2d552567 |
13
.gitignore
vendored
13
.gitignore
vendored
@ -1,13 +0,0 @@
|
||||
.DS_Store
|
||||
/obitools.test/
|
||||
/OBITools3- 1.01.16/
|
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/OBITools3-0.00.0/
|
||||
/build/
|
||||
/testpip/
|
||||
/toto.obidms/
|
||||
/unittests/
|
||||
/setup.py.old
|
||||
/3_Hornung_testseq.fastq
|
||||
/sample/
|
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/save.temp/
|
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/obitmp/
|
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17
.project
17
.project
@ -1,17 +0,0 @@
|
||||
<?xml version="1.0" encoding="UTF-8"?>
|
||||
<projectDescription>
|
||||
<name>obitools3</name>
|
||||
<comment></comment>
|
||||
<projects>
|
||||
</projects>
|
||||
<buildSpec>
|
||||
<buildCommand>
|
||||
<name>org.python.pydev.PyDevBuilder</name>
|
||||
<arguments>
|
||||
</arguments>
|
||||
</buildCommand>
|
||||
</buildSpec>
|
||||
<natures>
|
||||
<nature>org.python.pydev.pythonNature</nature>
|
||||
</natures>
|
||||
</projectDescription>
|
||||
@ -1,20 +0,0 @@
|
||||
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
|
||||
<?eclipse-pydev version="1.0"?><pydev_project>
|
||||
|
||||
|
||||
<pydev_property name="org.python.pydev.PYTHON_PROJECT_INTERPRETER">python3.6-obitool3</pydev_property>
|
||||
|
||||
|
||||
<pydev_property name="org.python.pydev.PYTHON_PROJECT_VERSION">python interpreter</pydev_property>
|
||||
|
||||
|
||||
<pydev_pathproperty name="org.python.pydev.PROJECT_SOURCE_PATH">
|
||||
|
||||
|
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<path>/${PROJECT_DIR_NAME}/python</path>
|
||||
|
||||
|
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</pydev_pathproperty>
|
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|
||||
|
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</pydev_project>
|
||||
506
Licence_CeCILL_V2-en.txt
Normal file
506
Licence_CeCILL_V2-en.txt
Normal file
@ -0,0 +1,506 @@
|
||||
|
||||
CeCILL FREE SOFTWARE LICENSE AGREEMENT
|
||||
|
||||
|
||||
Notice
|
||||
|
||||
This Agreement is a Free Software license agreement that is the result
|
||||
of discussions between its authors in order to ensure compliance with
|
||||
the two main principles guiding its drafting:
|
||||
|
||||
* firstly, compliance with the principles governing the distribution
|
||||
of Free Software: access to source code, broad rights granted to
|
||||
users,
|
||||
* secondly, the election of a governing law, French law, with which
|
||||
it is conformant, both as regards the law of torts and
|
||||
intellectual property law, and the protection that it offers to
|
||||
both authors and holders of the economic rights over software.
|
||||
|
||||
The authors of the CeCILL (for Ce[a] C[nrs] I[nria] L[ogiciel] L[ibre])
|
||||
license are:
|
||||
|
||||
Commissariat <20> l'Energie Atomique - CEA, a public scientific, technical
|
||||
and industrial research establishment, having its principal place of
|
||||
business at 25 rue Leblanc, immeuble Le Ponant D, 75015 Paris, France.
|
||||
|
||||
Centre National de la Recherche Scientifique - CNRS, a public scientific
|
||||
and technological establishment, having its principal place of business
|
||||
at 3 rue Michel-Ange, 75794 Paris cedex 16, France.
|
||||
|
||||
Institut National de Recherche en Informatique et en Automatique -
|
||||
INRIA, a public scientific and technological establishment, having its
|
||||
principal place of business at Domaine de Voluceau, Rocquencourt, BP
|
||||
105, 78153 Le Chesnay cedex, France.
|
||||
|
||||
|
||||
Preamble
|
||||
|
||||
The purpose of this Free Software license agreement is to grant users
|
||||
the right to modify and redistribute the software governed by this
|
||||
license within the framework of an open source distribution model.
|
||||
|
||||
The exercising of these rights is conditional upon certain obligations
|
||||
for users so as to preserve this status for all subsequent redistributions.
|
||||
|
||||
In consideration of access to the source code and the rights to copy,
|
||||
modify and redistribute granted by the license, users are provided only
|
||||
with a limited warranty and the software's author, the holder of the
|
||||
economic rights, and the successive licensors only have limited liability.
|
||||
|
||||
In this respect, the risks associated with loading, using, modifying
|
||||
and/or developing or reproducing the software by the user are brought to
|
||||
the user's attention, given its Free Software status, which may make it
|
||||
complicated to use, with the result that its use is reserved for
|
||||
developers and experienced professionals having in-depth computer
|
||||
knowledge. Users are therefore encouraged to load and test the
|
||||
suitability of the software as regards their requirements in conditions
|
||||
enabling the security of their systems and/or data to be ensured and,
|
||||
more generally, to use and operate it in the same conditions of
|
||||
security. This Agreement may be freely reproduced and published,
|
||||
provided it is not altered, and that no provisions are either added or
|
||||
removed herefrom.
|
||||
|
||||
This Agreement may apply to any or all software for which the holder of
|
||||
the economic rights decides to submit the use thereof to its provisions.
|
||||
|
||||
|
||||
Article 1 - DEFINITIONS
|
||||
|
||||
For the purpose of this Agreement, when the following expressions
|
||||
commence with a capital letter, they shall have the following meaning:
|
||||
|
||||
Agreement: means this license agreement, and its possible subsequent
|
||||
versions and annexes.
|
||||
|
||||
Software: means the software in its Object Code and/or Source Code form
|
||||
and, where applicable, its documentation, "as is" when the Licensee
|
||||
accepts the Agreement.
|
||||
|
||||
Initial Software: means the Software in its Source Code and possibly its
|
||||
Object Code form and, where applicable, its documentation, "as is" when
|
||||
it is first distributed under the terms and conditions of the Agreement.
|
||||
|
||||
Modified Software: means the Software modified by at least one
|
||||
Contribution.
|
||||
|
||||
Source Code: means all the Software's instructions and program lines to
|
||||
which access is required so as to modify the Software.
|
||||
|
||||
Object Code: means the binary files originating from the compilation of
|
||||
the Source Code.
|
||||
|
||||
Holder: means the holder(s) of the economic rights over the Initial
|
||||
Software.
|
||||
|
||||
Licensee: means the Software user(s) having accepted the Agreement.
|
||||
|
||||
Contributor: means a Licensee having made at least one Contribution.
|
||||
|
||||
Licensor: means the Holder, or any other individual or legal entity, who
|
||||
distributes the Software under the Agreement.
|
||||
|
||||
Contribution: means any or all modifications, corrections, translations,
|
||||
adaptations and/or new functions integrated into the Software by any or
|
||||
all Contributors, as well as any or all Internal Modules.
|
||||
|
||||
Module: means a set of sources files including their documentation that
|
||||
enables supplementary functions or services in addition to those offered
|
||||
by the Software.
|
||||
|
||||
External Module: means any or all Modules, not derived from the
|
||||
Software, so that this Module and the Software run in separate address
|
||||
spaces, with one calling the other when they are run.
|
||||
|
||||
Internal Module: means any or all Module, connected to the Software so
|
||||
that they both execute in the same address space.
|
||||
|
||||
GNU GPL: means the GNU General Public License version 2 or any
|
||||
subsequent version, as published by the Free Software Foundation Inc.
|
||||
|
||||
Parties: mean both the Licensee and the Licensor.
|
||||
|
||||
These expressions may be used both in singular and plural form.
|
||||
|
||||
|
||||
Article 2 - PURPOSE
|
||||
|
||||
The purpose of the Agreement is the grant by the Licensor to the
|
||||
Licensee of a non-exclusive, transferable and worldwide license for the
|
||||
Software as set forth in Article 5 hereinafter for the whole term of the
|
||||
protection granted by the rights over said Software.
|
||||
|
||||
|
||||
Article 3 - ACCEPTANCE
|
||||
|
||||
3.1 The Licensee shall be deemed as having accepted the terms and
|
||||
conditions of this Agreement upon the occurrence of the first of the
|
||||
following events:
|
||||
|
||||
* (i) loading the Software by any or all means, notably, by
|
||||
downloading from a remote server, or by loading from a physical
|
||||
medium;
|
||||
* (ii) the first time the Licensee exercises any of the rights
|
||||
granted hereunder.
|
||||
|
||||
3.2 One copy of the Agreement, containing a notice relating to the
|
||||
characteristics of the Software, to the limited warranty, and to the
|
||||
fact that its use is restricted to experienced users has been provided
|
||||
to the Licensee prior to its acceptance as set forth in Article 3.1
|
||||
hereinabove, and the Licensee hereby acknowledges that it has read and
|
||||
understood it.
|
||||
|
||||
|
||||
Article 4 - EFFECTIVE DATE AND TERM
|
||||
|
||||
|
||||
4.1 EFFECTIVE DATE
|
||||
|
||||
The Agreement shall become effective on the date when it is accepted by
|
||||
the Licensee as set forth in Article 3.1.
|
||||
|
||||
|
||||
4.2 TERM
|
||||
|
||||
The Agreement shall remain in force for the entire legal term of
|
||||
protection of the economic rights over the Software.
|
||||
|
||||
|
||||
Article 5 - SCOPE OF RIGHTS GRANTED
|
||||
|
||||
The Licensor hereby grants to the Licensee, who accepts, the following
|
||||
rights over the Software for any or all use, and for the term of the
|
||||
Agreement, on the basis of the terms and conditions set forth hereinafter.
|
||||
|
||||
Besides, if the Licensor owns or comes to own one or more patents
|
||||
protecting all or part of the functions of the Software or of its
|
||||
components, the Licensor undertakes not to enforce the rights granted by
|
||||
these patents against successive Licensees using, exploiting or
|
||||
modifying the Software. If these patents are transferred, the Licensor
|
||||
undertakes to have the transferees subscribe to the obligations set
|
||||
forth in this paragraph.
|
||||
|
||||
|
||||
5.1 RIGHT OF USE
|
||||
|
||||
The Licensee is authorized to use the Software, without any limitation
|
||||
as to its fields of application, with it being hereinafter specified
|
||||
that this comprises:
|
||||
|
||||
1. permanent or temporary reproduction of all or part of the Software
|
||||
by any or all means and in any or all form.
|
||||
|
||||
2. loading, displaying, running, or storing the Software on any or
|
||||
all medium.
|
||||
|
||||
3. entitlement to observe, study or test its operation so as to
|
||||
determine the ideas and principles behind any or all constituent
|
||||
elements of said Software. This shall apply when the Licensee
|
||||
carries out any or all loading, displaying, running, transmission
|
||||
or storage operation as regards the Software, that it is entitled
|
||||
to carry out hereunder.
|
||||
|
||||
|
||||
5.2 ENTITLEMENT TO MAKE CONTRIBUTIONS
|
||||
|
||||
The right to make Contributions includes the right to translate, adapt,
|
||||
arrange, or make any or all modifications to the Software, and the right
|
||||
to reproduce the resulting software.
|
||||
|
||||
The Licensee is authorized to make any or all Contributions to the
|
||||
Software provided that it includes an explicit notice that it is the
|
||||
author of said Contribution and indicates the date of the creation thereof.
|
||||
|
||||
|
||||
5.3 RIGHT OF DISTRIBUTION
|
||||
|
||||
In particular, the right of distribution includes the right to publish,
|
||||
transmit and communicate the Software to the general public on any or
|
||||
all medium, and by any or all means, and the right to market, either in
|
||||
consideration of a fee, or free of charge, one or more copies of the
|
||||
Software by any means.
|
||||
|
||||
The Licensee is further authorized to distribute copies of the modified
|
||||
or unmodified Software to third parties according to the terms and
|
||||
conditions set forth hereinafter.
|
||||
|
||||
|
||||
5.3.1 DISTRIBUTION OF SOFTWARE WITHOUT MODIFICATION
|
||||
|
||||
The Licensee is authorized to distribute true copies of the Software in
|
||||
Source Code or Object Code form, provided that said distribution
|
||||
complies with all the provisions of the Agreement and is accompanied by:
|
||||
|
||||
1. a copy of the Agreement,
|
||||
|
||||
2. a notice relating to the limitation of both the Licensor's
|
||||
warranty and liability as set forth in Articles 8 and 9,
|
||||
|
||||
and that, in the event that only the Object Code of the Software is
|
||||
redistributed, the Licensee allows future Licensees unhindered access to
|
||||
the full Source Code of the Software by indicating how to access it, it
|
||||
being understood that the additional cost of acquiring the Source Code
|
||||
shall not exceed the cost of transferring the data.
|
||||
|
||||
|
||||
5.3.2 DISTRIBUTION OF MODIFIED SOFTWARE
|
||||
|
||||
When the Licensee makes a Contribution to the Software, the terms and
|
||||
conditions for the distribution of the resulting Modified Software
|
||||
become subject to all the provisions of this Agreement.
|
||||
|
||||
The Licensee is authorized to distribute the Modified Software, in
|
||||
source code or object code form, provided that said distribution
|
||||
complies with all the provisions of the Agreement and is accompanied by:
|
||||
|
||||
1. a copy of the Agreement,
|
||||
|
||||
2. a notice relating to the limitation of both the Licensor's
|
||||
warranty and liability as set forth in Articles 8 and 9,
|
||||
|
||||
and that, in the event that only the object code of the Modified
|
||||
Software is redistributed, the Licensee allows future Licensees
|
||||
unhindered access to the full source code of the Modified Software by
|
||||
indicating how to access it, it being understood that the additional
|
||||
cost of acquiring the source code shall not exceed the cost of
|
||||
transferring the data.
|
||||
|
||||
|
||||
5.3.3 DISTRIBUTION OF EXTERNAL MODULES
|
||||
|
||||
When the Licensee has developed an External Module, the terms and
|
||||
conditions of this Agreement do not apply to said External Module, that
|
||||
may be distributed under a separate license agreement.
|
||||
|
||||
|
||||
5.3.4 COMPATIBILITY WITH THE GNU GPL
|
||||
|
||||
The Licensee can include a code that is subject to the provisions of one
|
||||
of the versions of the GNU GPL in the Modified or unmodified Software,
|
||||
and distribute that entire code under the terms of the same version of
|
||||
the GNU GPL.
|
||||
|
||||
The Licensee can include the Modified or unmodified Software in a code
|
||||
that is subject to the provisions of one of the versions of the GNU GPL,
|
||||
and distribute that entire code under the terms of the same version of
|
||||
the GNU GPL.
|
||||
|
||||
|
||||
Article 6 - INTELLECTUAL PROPERTY
|
||||
|
||||
|
||||
6.1 OVER THE INITIAL SOFTWARE
|
||||
|
||||
The Holder owns the economic rights over the Initial Software. Any or
|
||||
all use of the Initial Software is subject to compliance with the terms
|
||||
and conditions under which the Holder has elected to distribute its work
|
||||
and no one shall be entitled to modify the terms and conditions for the
|
||||
distribution of said Initial Software.
|
||||
|
||||
The Holder undertakes that the Initial Software will remain ruled at
|
||||
least by this Agreement, for the duration set forth in Article 4.2.
|
||||
|
||||
|
||||
6.2 OVER THE CONTRIBUTIONS
|
||||
|
||||
The Licensee who develops a Contribution is the owner of the
|
||||
intellectual property rights over this Contribution as defined by
|
||||
applicable law.
|
||||
|
||||
|
||||
6.3 OVER THE EXTERNAL MODULES
|
||||
|
||||
The Licensee who develops an External Module is the owner of the
|
||||
intellectual property rights over this External Module as defined by
|
||||
applicable law and is free to choose the type of agreement that shall
|
||||
govern its distribution.
|
||||
|
||||
|
||||
6.4 JOINT PROVISIONS
|
||||
|
||||
The Licensee expressly undertakes:
|
||||
|
||||
1. not to remove, or modify, in any manner, the intellectual property
|
||||
notices attached to the Software;
|
||||
|
||||
2. to reproduce said notices, in an identical manner, in the copies
|
||||
of the Software modified or not.
|
||||
|
||||
The Licensee undertakes not to directly or indirectly infringe the
|
||||
intellectual property rights of the Holder and/or Contributors on the
|
||||
Software and to take, where applicable, vis-<2D>-vis its staff, any and all
|
||||
measures required to ensure respect of said intellectual property rights
|
||||
of the Holder and/or Contributors.
|
||||
|
||||
|
||||
Article 7 - RELATED SERVICES
|
||||
|
||||
7.1 Under no circumstances shall the Agreement oblige the Licensor to
|
||||
provide technical assistance or maintenance services for the Software.
|
||||
|
||||
However, the Licensor is entitled to offer this type of services. The
|
||||
terms and conditions of such technical assistance, and/or such
|
||||
maintenance, shall be set forth in a separate instrument. Only the
|
||||
Licensor offering said maintenance and/or technical assistance services
|
||||
shall incur liability therefor.
|
||||
|
||||
7.2 Similarly, any Licensor is entitled to offer to its licensees, under
|
||||
its sole responsibility, a warranty, that shall only be binding upon
|
||||
itself, for the redistribution of the Software and/or the Modified
|
||||
Software, under terms and conditions that it is free to decide. Said
|
||||
warranty, and the financial terms and conditions of its application,
|
||||
shall be subject of a separate instrument executed between the Licensor
|
||||
and the Licensee.
|
||||
|
||||
|
||||
Article 8 - LIABILITY
|
||||
|
||||
8.1 Subject to the provisions of Article 8.2, the Licensee shall be
|
||||
entitled to claim compensation for any direct loss it may have suffered
|
||||
from the Software as a result of a fault on the part of the relevant
|
||||
Licensor, subject to providing evidence thereof.
|
||||
|
||||
8.2 The Licensor's liability is limited to the commitments made under
|
||||
this Agreement and shall not be incurred as a result of in particular:
|
||||
(i) loss due the Licensee's total or partial failure to fulfill its
|
||||
obligations, (ii) direct or consequential loss that is suffered by the
|
||||
Licensee due to the use or performance of the Software, and (iii) more
|
||||
generally, any consequential loss. In particular the Parties expressly
|
||||
agree that any or all pecuniary or business loss (i.e. loss of data,
|
||||
loss of profits, operating loss, loss of customers or orders,
|
||||
opportunity cost, any disturbance to business activities) or any or all
|
||||
legal proceedings instituted against the Licensee by a third party,
|
||||
shall constitute consequential loss and shall not provide entitlement to
|
||||
any or all compensation from the Licensor.
|
||||
|
||||
|
||||
Article 9 - WARRANTY
|
||||
|
||||
9.1 The Licensee acknowledges that the scientific and technical
|
||||
state-of-the-art when the Software was distributed did not enable all
|
||||
possible uses to be tested and verified, nor for the presence of
|
||||
possible defects to be detected. In this respect, the Licensee's
|
||||
attention has been drawn to the risks associated with loading, using,
|
||||
modifying and/or developing and reproducing the Software which are
|
||||
reserved for experienced users.
|
||||
|
||||
The Licensee shall be responsible for verifying, by any or all means,
|
||||
the suitability of the product for its requirements, its good working
|
||||
order, and for ensuring that it shall not cause damage to either persons
|
||||
or properties.
|
||||
|
||||
9.2 The Licensor hereby represents, in good faith, that it is entitled
|
||||
to grant all the rights over the Software (including in particular the
|
||||
rights set forth in Article 5).
|
||||
|
||||
9.3 The Licensee acknowledges that the Software is supplied "as is" by
|
||||
the Licensor without any other express or tacit warranty, other than
|
||||
that provided for in Article 9.2 and, in particular, without any warranty
|
||||
as to its commercial value, its secured, safe, innovative or relevant
|
||||
nature.
|
||||
|
||||
Specifically, the Licensor does not warrant that the Software is free
|
||||
from any error, that it will operate without interruption, that it will
|
||||
be compatible with the Licensee's own equipment and software
|
||||
configuration, nor that it will meet the Licensee's requirements.
|
||||
|
||||
9.4 The Licensor does not either expressly or tacitly warrant that the
|
||||
Software does not infringe any third party intellectual property right
|
||||
relating to a patent, software or any other property right. Therefore,
|
||||
the Licensor disclaims any and all liability towards the Licensee
|
||||
arising out of any or all proceedings for infringement that may be
|
||||
instituted in respect of the use, modification and redistribution of the
|
||||
Software. Nevertheless, should such proceedings be instituted against
|
||||
the Licensee, the Licensor shall provide it with technical and legal
|
||||
assistance for its defense. Such technical and legal assistance shall be
|
||||
decided on a case-by-case basis between the relevant Licensor and the
|
||||
Licensee pursuant to a memorandum of understanding. The Licensor
|
||||
disclaims any and all liability as regards the Licensee's use of the
|
||||
name of the Software. No warranty is given as regards the existence of
|
||||
prior rights over the name of the Software or as regards the existence
|
||||
of a trademark.
|
||||
|
||||
|
||||
Article 10 - TERMINATION
|
||||
|
||||
10.1 In the event of a breach by the Licensee of its obligations
|
||||
hereunder, the Licensor may automatically terminate this Agreement
|
||||
thirty (30) days after notice has been sent to the Licensee and has
|
||||
remained ineffective.
|
||||
|
||||
10.2 A Licensee whose Agreement is terminated shall no longer be
|
||||
authorized to use, modify or distribute the Software. However, any
|
||||
licenses that it may have granted prior to termination of the Agreement
|
||||
shall remain valid subject to their having been granted in compliance
|
||||
with the terms and conditions hereof.
|
||||
|
||||
|
||||
Article 11 - MISCELLANEOUS
|
||||
|
||||
|
||||
11.1 EXCUSABLE EVENTS
|
||||
|
||||
Neither Party shall be liable for any or all delay, or failure to
|
||||
perform the Agreement, that may be attributable to an event of force
|
||||
majeure, an act of God or an outside cause, such as defective
|
||||
functioning or interruptions of the electricity or telecommunications
|
||||
networks, network paralysis following a virus attack, intervention by
|
||||
government authorities, natural disasters, water damage, earthquakes,
|
||||
fire, explosions, strikes and labor unrest, war, etc.
|
||||
|
||||
11.2 Any failure by either Party, on one or more occasions, to invoke
|
||||
one or more of the provisions hereof, shall under no circumstances be
|
||||
interpreted as being a waiver by the interested Party of its right to
|
||||
invoke said provision(s) subsequently.
|
||||
|
||||
11.3 The Agreement cancels and replaces any or all previous agreements,
|
||||
whether written or oral, between the Parties and having the same
|
||||
purpose, and constitutes the entirety of the agreement between said
|
||||
Parties concerning said purpose. No supplement or modification to the
|
||||
terms and conditions hereof shall be effective as between the Parties
|
||||
unless it is made in writing and signed by their duly authorized
|
||||
representatives.
|
||||
|
||||
11.4 In the event that one or more of the provisions hereof were to
|
||||
conflict with a current or future applicable act or legislative text,
|
||||
said act or legislative text shall prevail, and the Parties shall make
|
||||
the necessary amendments so as to comply with said act or legislative
|
||||
text. All other provisions shall remain effective. Similarly, invalidity
|
||||
of a provision of the Agreement, for any reason whatsoever, shall not
|
||||
cause the Agreement as a whole to be invalid.
|
||||
|
||||
|
||||
11.5 LANGUAGE
|
||||
|
||||
The Agreement is drafted in both French and English and both versions
|
||||
are deemed authentic.
|
||||
|
||||
|
||||
Article 12 - NEW VERSIONS OF THE AGREEMENT
|
||||
|
||||
12.1 Any person is authorized to duplicate and distribute copies of this
|
||||
Agreement.
|
||||
|
||||
12.2 So as to ensure coherence, the wording of this Agreement is
|
||||
protected and may only be modified by the authors of the License, who
|
||||
reserve the right to periodically publish updates or new versions of the
|
||||
Agreement, each with a separate number. These subsequent versions may
|
||||
address new issues encountered by Free Software.
|
||||
|
||||
12.3 Any Software distributed under a given version of the Agreement may
|
||||
only be subsequently distributed under the same version of the Agreement
|
||||
or a subsequent version, subject to the provisions of Article 5.3.4.
|
||||
|
||||
|
||||
Article 13 - GOVERNING LAW AND JURISDICTION
|
||||
|
||||
13.1 The Agreement is governed by French law. The Parties agree to
|
||||
endeavor to seek an amicable solution to any disagreements or disputes
|
||||
that may arise during the performance of the Agreement.
|
||||
|
||||
13.2 Failing an amicable solution within two (2) months as from their
|
||||
occurrence, and unless emergency proceedings are necessary, the
|
||||
disagreements or disputes shall be referred to the Paris Courts having
|
||||
jurisdiction, by the more diligent Party.
|
||||
|
||||
|
||||
Version 2.0 dated 2006-09-05.
|
||||
512
Licence_CeCILL_V2-fr.txt
Normal file
512
Licence_CeCILL_V2-fr.txt
Normal file
@ -0,0 +1,512 @@
|
||||
|
||||
CONTRAT DE LICENCE DE LOGICIEL LIBRE CeCILL
|
||||
|
||||
|
||||
Avertissement
|
||||
|
||||
Ce contrat est une licence de logiciel libre issue d'une concertation
|
||||
entre ses auteurs afin que le respect de deux grands principes pr<70>side <20>
|
||||
sa r<>daction:
|
||||
|
||||
* d'une part, le respect des principes de diffusion des logiciels
|
||||
libres: acc<63>s au code source, droits <20>tendus conf<6E>r<EFBFBD>s aux
|
||||
utilisateurs,
|
||||
* d'autre part, la d<>signation d'un droit applicable, le droit
|
||||
fran<61>ais, auquel elle est conforme, tant au regard du droit de la
|
||||
responsabilit<69> civile que du droit de la propri<72>t<EFBFBD> intellectuelle
|
||||
et de la protection qu'il offre aux auteurs et titulaires des
|
||||
droits patrimoniaux sur un logiciel.
|
||||
|
||||
Les auteurs de la licence CeCILL (pour Ce[a] C[nrs] I[nria] L[ogiciel]
|
||||
L[ibre]) sont:
|
||||
|
||||
Commissariat <20> l'Energie Atomique - CEA, <20>tablissement public de
|
||||
recherche <20> caract<63>re scientifique, technique et industriel, dont le
|
||||
si<EFBFBD>ge est situ<74> 25 rue Leblanc, immeuble Le Ponant D, 75015 Paris.
|
||||
|
||||
Centre National de la Recherche Scientifique - CNRS, <20>tablissement
|
||||
public <20> caract<63>re scientifique et technologique, dont le si<73>ge est
|
||||
situ<EFBFBD> 3 rue Michel-Ange, 75794 Paris cedex 16.
|
||||
|
||||
Institut National de Recherche en Informatique et en Automatique -
|
||||
INRIA, <20>tablissement public <20> caract<63>re scientifique et technologique,
|
||||
dont le si<73>ge est situ<74> Domaine de Voluceau, Rocquencourt, BP 105, 78153
|
||||
Le Chesnay cedex.
|
||||
|
||||
|
||||
Pr<50>ambule
|
||||
|
||||
Ce contrat est une licence de logiciel libre dont l'objectif est de
|
||||
conf<EFBFBD>rer aux utilisateurs la libert<72> de modification et de
|
||||
redistribution du logiciel r<>gi par cette licence dans le cadre d'un
|
||||
mod<EFBFBD>le de diffusion en logiciel libre.
|
||||
|
||||
L'exercice de ces libert<72>s est assorti de certains devoirs <20> la charge
|
||||
des utilisateurs afin de pr<70>server ce statut au cours des
|
||||
redistributions ult<6C>rieures.
|
||||
|
||||
L'accessibilit<69> au code source et les droits de copie, de modification
|
||||
et de redistribution qui en d<>coulent ont pour contrepartie de n'offrir
|
||||
aux utilisateurs qu'une garantie limit<69>e et de ne faire peser sur
|
||||
l'auteur du logiciel, le titulaire des droits patrimoniaux et les
|
||||
conc<EFBFBD>dants successifs qu'une responsabilit<69> restreinte.
|
||||
|
||||
A cet <20>gard l'attention de l'utilisateur est attir<69>e sur les risques
|
||||
associ<EFBFBD>s au chargement, <20> l'utilisation, <20> la modification et/ou au
|
||||
d<EFBFBD>veloppement et <20> la reproduction du logiciel par l'utilisateur <20>tant
|
||||
donn<EFBFBD> sa sp<73>cificit<69> de logiciel libre, qui peut le rendre complexe <20>
|
||||
manipuler et qui le r<>serve donc <20> des d<>veloppeurs ou des
|
||||
professionnels avertis poss<73>dant des connaissances informatiques
|
||||
approfondies. Les utilisateurs sont donc invit<69>s <20> charger et tester
|
||||
l'ad<61>quation du logiciel <20> leurs besoins dans des conditions permettant
|
||||
d'assurer la s<>curit<69> de leurs syst<73>mes et/ou de leurs donn<6E>es et, plus
|
||||
g<EFBFBD>n<EFBFBD>ralement, <20> l'utiliser et l'exploiter dans les m<>mes conditions de
|
||||
s<EFBFBD>curit<EFBFBD>. Ce contrat peut <20>tre reproduit et diffus<75> librement, sous
|
||||
r<EFBFBD>serve de le conserver en l'<27>tat, sans ajout ni suppression de clauses.
|
||||
|
||||
Ce contrat est susceptible de s'appliquer <20> tout logiciel dont le
|
||||
titulaire des droits patrimoniaux d<>cide de soumettre l'exploitation aux
|
||||
dispositions qu'il contient.
|
||||
|
||||
|
||||
Article 1 - DEFINITIONS
|
||||
|
||||
Dans ce contrat, les termes suivants, lorsqu'ils seront <20>crits avec une
|
||||
lettre capitale, auront la signification suivante:
|
||||
|
||||
Contrat: d<>signe le pr<70>sent contrat de licence, ses <20>ventuelles versions
|
||||
post<EFBFBD>rieures et annexes.
|
||||
|
||||
Logiciel: d<>signe le logiciel sous sa forme de Code Objet et/ou de Code
|
||||
Source et le cas <20>ch<63>ant sa documentation, dans leur <20>tat au moment de
|
||||
l'acceptation du Contrat par le Licenci<63>.
|
||||
|
||||
Logiciel Initial: d<>signe le Logiciel sous sa forme de Code Source et
|
||||
<EFBFBD>ventuellement de Code Objet et le cas <20>ch<63>ant sa documentation, dans
|
||||
leur <20>tat au moment de leur premi<6D>re diffusion sous les termes du Contrat.
|
||||
|
||||
Logiciel Modifi<66>: d<>signe le Logiciel modifi<66> par au moins une
|
||||
Contribution.
|
||||
|
||||
Code Source: d<>signe l'ensemble des instructions et des lignes de
|
||||
programme du Logiciel et auquel l'acc<63>s est n<>cessaire en vue de
|
||||
modifier le Logiciel.
|
||||
|
||||
Code Objet: d<>signe les fichiers binaires issus de la compilation du
|
||||
Code Source.
|
||||
|
||||
Titulaire: d<>signe le ou les d<>tenteurs des droits patrimoniaux d'auteur
|
||||
sur le Logiciel Initial.
|
||||
|
||||
Licenci<EFBFBD>: d<>signe le ou les utilisateurs du Logiciel ayant accept<70> le
|
||||
Contrat.
|
||||
|
||||
Contributeur: d<>signe le Licenci<63> auteur d'au moins une Contribution.
|
||||
|
||||
Conc<EFBFBD>dant: d<>signe le Titulaire ou toute personne physique ou morale
|
||||
distribuant le Logiciel sous le Contrat.
|
||||
|
||||
Contribution: d<>signe l'ensemble des modifications, corrections,
|
||||
traductions, adaptations et/ou nouvelles fonctionnalit<69>s int<6E>gr<67>es dans
|
||||
le Logiciel par tout Contributeur, ainsi que tout Module Interne.
|
||||
|
||||
Module: d<>signe un ensemble de fichiers sources y compris leur
|
||||
documentation qui permet de r<>aliser des fonctionnalit<69>s ou services
|
||||
suppl<EFBFBD>mentaires <20> ceux fournis par le Logiciel.
|
||||
|
||||
Module Externe: d<>signe tout Module, non d<>riv<69> du Logiciel, tel que ce
|
||||
Module et le Logiciel s'ex<65>cutent dans des espaces d'adressage
|
||||
diff<EFBFBD>rents, l'un appelant l'autre au moment de leur ex<65>cution.
|
||||
|
||||
Module Interne: d<>signe tout Module li<6C> au Logiciel de telle sorte
|
||||
qu'ils s'ex<65>cutent dans le m<>me espace d'adressage.
|
||||
|
||||
GNU GPL: d<>signe la GNU General Public License dans sa version 2 ou
|
||||
toute version ult<6C>rieure, telle que publi<6C>e par Free Software Foundation
|
||||
Inc.
|
||||
|
||||
Parties: d<>signe collectivement le Licenci<63> et le Conc<6E>dant.
|
||||
|
||||
Ces termes s'entendent au singulier comme au pluriel.
|
||||
|
||||
|
||||
Article 2 - OBJET
|
||||
|
||||
Le Contrat a pour objet la concession par le Conc<6E>dant au Licenci<63> d'une
|
||||
licence non exclusive, cessible et mondiale du Logiciel telle que
|
||||
d<EFBFBD>finie ci-apr<70>s <20> l'article 5 pour toute la dur<75>e de protection des droits
|
||||
portant sur ce Logiciel.
|
||||
|
||||
|
||||
Article 3 - ACCEPTATION
|
||||
|
||||
3.1 L'acceptation par le Licenci<63> des termes du Contrat est r<>put<75>e
|
||||
acquise du fait du premier des faits suivants:
|
||||
|
||||
* (i) le chargement du Logiciel par tout moyen notamment par
|
||||
t<>l<EFBFBD>chargement <20> partir d'un serveur distant ou par chargement <20>
|
||||
partir d'un support physique;
|
||||
* (ii) le premier exercice par le Licenci<63> de l'un quelconque des
|
||||
droits conc<6E>d<EFBFBD>s par le Contrat.
|
||||
|
||||
3.2 Un exemplaire du Contrat, contenant notamment un avertissement
|
||||
relatif aux sp<73>cificit<69>s du Logiciel, <20> la restriction de garantie et <20>
|
||||
la limitation <20> un usage par des utilisateurs exp<78>riment<6E>s a <20>t<EFBFBD> mis <20>
|
||||
disposition du Licenci<63> pr<70>alablement <20> son acceptation telle que
|
||||
d<EFBFBD>finie <20> l'article 3.1 ci dessus et le Licenci<63> reconna<6E>t en avoir pris
|
||||
connaissance.
|
||||
|
||||
|
||||
Article 4 - ENTREE EN VIGUEUR ET DUREE
|
||||
|
||||
|
||||
4.1 ENTREE EN VIGUEUR
|
||||
|
||||
Le Contrat entre en vigueur <20> la date de son acceptation par le Licenci<63>
|
||||
telle que d<>finie en 3.1.
|
||||
|
||||
|
||||
4.2 DUREE
|
||||
|
||||
Le Contrat produira ses effets pendant toute la dur<75>e l<>gale de
|
||||
protection des droits patrimoniaux portant sur le Logiciel.
|
||||
|
||||
|
||||
Article 5 - ETENDUE DES DROITS CONCEDES
|
||||
|
||||
Le Conc<6E>dant conc<6E>de au Licenci<63>, qui accepte, les droits suivants sur
|
||||
le Logiciel pour toutes destinations et pour la dur<75>e du Contrat dans
|
||||
les conditions ci-apr<70>s d<>taill<6C>es.
|
||||
|
||||
Par ailleurs, si le Conc<6E>dant d<>tient ou venait <20> d<>tenir un ou
|
||||
plusieurs brevets d'invention prot<6F>geant tout ou partie des
|
||||
fonctionnalit<EFBFBD>s du Logiciel ou de ses composants, il s'engage <20> ne pas
|
||||
opposer les <20>ventuels droits conf<6E>r<EFBFBD>s par ces brevets aux Licenci<63>s
|
||||
successifs qui utiliseraient, exploiteraient ou modifieraient le
|
||||
Logiciel. En cas de cession de ces brevets, le Conc<6E>dant s'engage <20>
|
||||
faire reprendre les obligations du pr<70>sent alin<69>a aux cessionnaires.
|
||||
|
||||
|
||||
5.1 DROIT D'UTILISATION
|
||||
|
||||
Le Licenci<63> est autoris<69> <20> utiliser le Logiciel, sans restriction quant
|
||||
aux domaines d'application, <20>tant ci-apr<70>s pr<70>cis<69> que cela comporte:
|
||||
|
||||
1. la reproduction permanente ou provisoire du Logiciel en tout ou
|
||||
partie par tout moyen et sous toute forme.
|
||||
|
||||
2. le chargement, l'affichage, l'ex<65>cution, ou le stockage du
|
||||
Logiciel sur tout support.
|
||||
|
||||
3. la possibilit<69> d'en observer, d'en <20>tudier, ou d'en tester le
|
||||
fonctionnement afin de d<>terminer les id<69>es et principes qui sont
|
||||
<20> la base de n'importe quel <20>l<EFBFBD>ment de ce Logiciel; et ceci,
|
||||
lorsque le Licenci<63> effectue toute op<6F>ration de chargement,
|
||||
d'affichage, d'ex<65>cution, de transmission ou de stockage du
|
||||
Logiciel qu'il est en droit d'effectuer en vertu du Contrat.
|
||||
|
||||
|
||||
5.2 DROIT D'APPORTER DES CONTRIBUTIONS
|
||||
|
||||
Le droit d'apporter des Contributions comporte le droit de traduire,
|
||||
d'adapter, d'arranger ou d'apporter toute autre modification au Logiciel
|
||||
et le droit de reproduire le logiciel en r<>sultant.
|
||||
|
||||
Le Licenci<63> est autoris<69> <20> apporter toute Contribution au Logiciel sous
|
||||
r<EFBFBD>serve de mentionner, de fa<66>on explicite, son nom en tant qu'auteur de
|
||||
cette Contribution et la date de cr<63>ation de celle-ci.
|
||||
|
||||
|
||||
5.3 DROIT DE DISTRIBUTION
|
||||
|
||||
Le droit de distribution comporte notamment le droit de diffuser, de
|
||||
transmettre et de communiquer le Logiciel au public sur tout support et
|
||||
par tout moyen ainsi que le droit de mettre sur le march<63> <20> titre
|
||||
on<EFBFBD>reux ou gratuit, un ou des exemplaires du Logiciel par tout proc<6F>d<EFBFBD>.
|
||||
|
||||
Le Licenci<63> est autoris<69> <20> distribuer des copies du Logiciel, modifi<66> ou
|
||||
non, <20> des tiers dans les conditions ci-apr<70>s d<>taill<6C>es.
|
||||
|
||||
|
||||
5.3.1 DISTRIBUTION DU LOGICIEL SANS MODIFICATION
|
||||
|
||||
Le Licenci<63> est autoris<69> <20> distribuer des copies conformes du Logiciel,
|
||||
sous forme de Code Source ou de Code Objet, <20> condition que cette
|
||||
distribution respecte les dispositions du Contrat dans leur totalit<69> et
|
||||
soit accompagn<67>e:
|
||||
|
||||
1. d'un exemplaire du Contrat,
|
||||
|
||||
2. d'un avertissement relatif <20> la restriction de garantie et de
|
||||
responsabilit<69> du Conc<6E>dant telle que pr<70>vue aux articles 8
|
||||
et 9,
|
||||
|
||||
et que, dans le cas o<> seul le Code Objet du Logiciel est redistribu<62>,
|
||||
le Licenci<63> permette aux futurs Licenci<63>s d'acc<63>der facilement au Code
|
||||
Source complet du Logiciel en indiquant les modalit<69>s d'acc<63>s, <20>tant
|
||||
entendu que le co<63>t additionnel d'acquisition du Code Source ne devra
|
||||
pas exc<78>der le simple co<63>t de transfert des donn<6E>es.
|
||||
|
||||
|
||||
5.3.2 DISTRIBUTION DU LOGICIEL MODIFIE
|
||||
|
||||
Lorsque le Licenci<63> apporte une Contribution au Logiciel, les conditions
|
||||
de distribution du Logiciel Modifi<66> en r<>sultant sont alors soumises <20>
|
||||
l'int<6E>gralit<69> des dispositions du Contrat.
|
||||
|
||||
Le Licenci<63> est autoris<69> <20> distribuer le Logiciel Modifi<66>, sous forme de
|
||||
code source ou de code objet, <20> condition que cette distribution
|
||||
respecte les dispositions du Contrat dans leur totalit<69> et soit
|
||||
accompagn<EFBFBD>e:
|
||||
|
||||
1. d'un exemplaire du Contrat,
|
||||
|
||||
2. d'un avertissement relatif <20> la restriction de garantie et de
|
||||
responsabilit<69> du Conc<6E>dant telle que pr<70>vue aux articles 8
|
||||
et 9,
|
||||
|
||||
et que, dans le cas o<> seul le code objet du Logiciel Modifi<66> est
|
||||
redistribu<EFBFBD>, le Licenci<63> permette aux futurs Licenci<63>s d'acc<63>der
|
||||
facilement au code source complet du Logiciel Modifi<66> en indiquant les
|
||||
modalit<EFBFBD>s d'acc<63>s, <20>tant entendu que le co<63>t additionnel d'acquisition
|
||||
du code source ne devra pas exc<78>der le simple co<63>t de transfert des donn<6E>es.
|
||||
|
||||
|
||||
5.3.3 DISTRIBUTION DES MODULES EXTERNES
|
||||
|
||||
Lorsque le Licenci<63> a d<>velopp<70> un Module Externe les conditions du
|
||||
Contrat ne s'appliquent pas <20> ce Module Externe, qui peut <20>tre distribu<62>
|
||||
sous un contrat de licence diff<66>rent.
|
||||
|
||||
|
||||
5.3.4 COMPATIBILITE AVEC LA LICENCE GNU GPL
|
||||
|
||||
Le Licenci<63> peut inclure un code soumis aux dispositions d'une des
|
||||
versions de la licence GNU GPL dans le Logiciel modifi<66> ou non et
|
||||
distribuer l'ensemble sous les conditions de la m<>me version de la
|
||||
licence GNU GPL.
|
||||
|
||||
Le Licenci<63> peut inclure le Logiciel modifi<66> ou non dans un code soumis
|
||||
aux dispositions d'une des versions de la licence GNU GPL et distribuer
|
||||
l'ensemble sous les conditions de la m<>me version de la licence GNU GPL.
|
||||
|
||||
|
||||
Article 6 - PROPRIETE INTELLECTUELLE
|
||||
|
||||
|
||||
6.1 SUR LE LOGICIEL INITIAL
|
||||
|
||||
Le Titulaire est d<>tenteur des droits patrimoniaux sur le Logiciel
|
||||
Initial. Toute utilisation du Logiciel Initial est soumise au respect
|
||||
des conditions dans lesquelles le Titulaire a choisi de diffuser son
|
||||
oeuvre et nul autre n'a la facult<6C> de modifier les conditions de
|
||||
diffusion de ce Logiciel Initial.
|
||||
|
||||
Le Titulaire s'engage <20> ce que le Logiciel Initial reste au moins r<>gi
|
||||
par le Contrat et ce, pour la dur<75>e vis<69>e <20> l'article 4.2.
|
||||
|
||||
|
||||
6.2 SUR LES CONTRIBUTIONS
|
||||
|
||||
Le Licenci<63> qui a d<>velopp<70> une Contribution est titulaire sur celle-ci
|
||||
des droits de propri<72>t<EFBFBD> intellectuelle dans les conditions d<>finies par
|
||||
la l<>gislation applicable.
|
||||
|
||||
|
||||
6.3 SUR LES MODULES EXTERNES
|
||||
|
||||
Le Licenci<63> qui a d<>velopp<70> un Module Externe est titulaire sur celui-ci
|
||||
des droits de propri<72>t<EFBFBD> intellectuelle dans les conditions d<>finies par
|
||||
la l<>gislation applicable et reste libre du choix du contrat r<>gissant
|
||||
sa diffusion.
|
||||
|
||||
|
||||
6.4 DISPOSITIONS COMMUNES
|
||||
|
||||
Le Licenci<63> s'engage express<73>ment:
|
||||
|
||||
1. <20> ne pas supprimer ou modifier de quelque mani<6E>re que ce soit les
|
||||
mentions de propri<72>t<EFBFBD> intellectuelle appos<6F>es sur le Logiciel;
|
||||
|
||||
2. <20> reproduire <20> l'identique lesdites mentions de propri<72>t<EFBFBD>
|
||||
intellectuelle sur les copies du Logiciel modifi<66> ou non.
|
||||
|
||||
Le Licenci<63> s'engage <20> ne pas porter atteinte, directement ou
|
||||
indirectement, aux droits de propri<72>t<EFBFBD> intellectuelle du Titulaire et/ou
|
||||
des Contributeurs sur le Logiciel et <20> prendre, le cas <20>ch<63>ant, <20>
|
||||
l'<27>gard de son personnel toutes les mesures n<>cessaires pour assurer le
|
||||
respect des dits droits de propri<72>t<EFBFBD> intellectuelle du Titulaire et/ou
|
||||
des Contributeurs.
|
||||
|
||||
|
||||
Article 7 - SERVICES ASSOCIES
|
||||
|
||||
7.1 Le Contrat n'oblige en aucun cas le Conc<6E>dant <20> la r<>alisation de
|
||||
prestations d'assistance technique ou de maintenance du Logiciel.
|
||||
|
||||
Cependant le Conc<6E>dant reste libre de proposer ce type de services. Les
|
||||
termes et conditions d'une telle assistance technique et/ou d'une telle
|
||||
maintenance seront alors d<>termin<69>s dans un acte s<>par<61>. Ces actes de
|
||||
maintenance et/ou assistance technique n'engageront que la seule
|
||||
responsabilit<EFBFBD> du Conc<6E>dant qui les propose.
|
||||
|
||||
7.2 De m<>me, tout Conc<6E>dant est libre de proposer, sous sa seule
|
||||
responsabilit<EFBFBD>, <20> ses licenci<63>s une garantie, qui n'engagera que lui,
|
||||
lors de la redistribution du Logiciel et/ou du Logiciel Modifi<66> et ce,
|
||||
dans les conditions qu'il souhaite. Cette garantie et les modalit<69>s
|
||||
financi<EFBFBD>res de son application feront l'objet d'un acte s<>par<61> entre le
|
||||
Conc<EFBFBD>dant et le Licenci<63>.
|
||||
|
||||
|
||||
Article 8 - RESPONSABILITE
|
||||
|
||||
8.1 Sous r<>serve des dispositions de l'article 8.2, le Licenci<63> a la
|
||||
facult<EFBFBD>, sous r<>serve de prouver la faute du Conc<6E>dant concern<72>, de
|
||||
solliciter la r<>paration du pr<70>judice direct qu'il subirait du fait du
|
||||
Logiciel et dont il apportera la preuve.
|
||||
|
||||
8.2 La responsabilit<69> du Conc<6E>dant est limit<69>e aux engagements pris en
|
||||
application du Contrat et ne saurait <20>tre engag<61>e en raison notamment:
|
||||
(i) des dommages dus <20> l'inex<65>cution, totale ou partielle, de ses
|
||||
obligations par le Licenci<63>, (ii) des dommages directs ou indirects
|
||||
d<EFBFBD>coulant de l'utilisation ou des performances du Logiciel subis par le
|
||||
Licenci<EFBFBD> et (iii) plus g<>n<EFBFBD>ralement d'un quelconque dommage indirect. En
|
||||
particulier, les Parties conviennent express<73>ment que tout pr<70>judice
|
||||
financier ou commercial (par exemple perte de donn<6E>es, perte de
|
||||
b<EFBFBD>n<EFBFBD>fices, perte d'exploitation, perte de client<6E>le ou de commandes,
|
||||
manque <20> gagner, trouble commercial quelconque) ou toute action dirig<69>e
|
||||
contre le Licenci<63> par un tiers, constitue un dommage indirect et
|
||||
n'ouvre pas droit <20> r<>paration par le Conc<6E>dant.
|
||||
|
||||
|
||||
Article 9 - GARANTIE
|
||||
|
||||
9.1 Le Licenci<63> reconna<6E>t que l'<27>tat actuel des connaissances
|
||||
scientifiques et techniques au moment de la mise en circulation du
|
||||
Logiciel ne permet pas d'en tester et d'en v<>rifier toutes les
|
||||
utilisations ni de d<>tecter l'existence d'<27>ventuels d<>fauts. L'attention
|
||||
du Licenci<63> a <20>t<EFBFBD> attir<69>e sur ce point sur les risques associ<63>s au
|
||||
chargement, <20> l'utilisation, la modification et/ou au d<>veloppement et <20>
|
||||
la reproduction du Logiciel qui sont r<>serv<72>s <20> des utilisateurs avertis.
|
||||
|
||||
Il rel<65>ve de la responsabilit<69> du Licenci<63> de contr<74>ler, par tous
|
||||
moyens, l'ad<61>quation du produit <20> ses besoins, son bon fonctionnement et
|
||||
de s'assurer qu'il ne causera pas de dommages aux personnes et aux biens.
|
||||
|
||||
9.2 Le Conc<6E>dant d<>clare de bonne foi <20>tre en droit de conc<6E>der
|
||||
l'ensemble des droits attach<63>s au Logiciel (comprenant notamment les
|
||||
droits vis<69>s <20> l'article 5).
|
||||
|
||||
9.3 Le Licenci<63> reconna<6E>t que le Logiciel est fourni "en l'<27>tat" par le
|
||||
Conc<EFBFBD>dant sans autre garantie, expresse ou tacite, que celle pr<70>vue <20>
|
||||
l'article 9.2 et notamment sans aucune garantie sur sa valeur commerciale,
|
||||
son caract<63>re s<>curis<69>, innovant ou pertinent.
|
||||
|
||||
En particulier, le Conc<6E>dant ne garantit pas que le Logiciel est exempt
|
||||
d'erreur, qu'il fonctionnera sans interruption, qu'il sera compatible
|
||||
avec l'<27>quipement du Licenci<63> et sa configuration logicielle ni qu'il
|
||||
remplira les besoins du Licenci<63>.
|
||||
|
||||
9.4 Le Conc<6E>dant ne garantit pas, de mani<6E>re expresse ou tacite, que le
|
||||
Logiciel ne porte pas atteinte <20> un quelconque droit de propri<72>t<EFBFBD>
|
||||
intellectuelle d'un tiers portant sur un brevet, un logiciel ou sur tout
|
||||
autre droit de propri<72>t<EFBFBD>. Ainsi, le Conc<6E>dant exclut toute garantie au
|
||||
profit du Licenci<63> contre les actions en contrefa<66>on qui pourraient <20>tre
|
||||
diligent<EFBFBD>es au titre de l'utilisation, de la modification, et de la
|
||||
redistribution du Logiciel. N<>anmoins, si de telles actions sont
|
||||
exerc<EFBFBD>es contre le Licenci<63>, le Conc<6E>dant lui apportera son aide
|
||||
technique et juridique pour sa d<>fense. Cette aide technique et
|
||||
juridique est d<>termin<69>e au cas par cas entre le Conc<6E>dant concern<72> et
|
||||
le Licenci<63> dans le cadre d'un protocole d'accord. Le Conc<6E>dant d<>gage
|
||||
toute responsabilit<69> quant <20> l'utilisation de la d<>nomination du
|
||||
Logiciel par le Licenci<63>. Aucune garantie n'est apport<72>e quant <20>
|
||||
l'existence de droits ant<6E>rieurs sur le nom du Logiciel et sur
|
||||
l'existence d'une marque.
|
||||
|
||||
|
||||
Article 10 - RESILIATION
|
||||
|
||||
10.1 En cas de manquement par le Licenci<63> aux obligations mises <20> sa
|
||||
charge par le Contrat, le Conc<6E>dant pourra r<>silier de plein droit le
|
||||
Contrat trente (30) jours apr<70>s notification adress<73>e au Licenci<63> et
|
||||
rest<EFBFBD>e sans effet.
|
||||
|
||||
10.2 Le Licenci<63> dont le Contrat est r<>sili<6C> n'est plus autoris<69> <20>
|
||||
utiliser, modifier ou distribuer le Logiciel. Cependant, toutes les
|
||||
licences qu'il aura conc<6E>d<EFBFBD>es ant<6E>rieurement <20> la r<>siliation du Contrat
|
||||
resteront valides sous r<>serve qu'elles aient <20>t<EFBFBD> effectu<74>es en
|
||||
conformit<EFBFBD> avec le Contrat.
|
||||
|
||||
|
||||
Article 11 - DISPOSITIONS DIVERSES
|
||||
|
||||
|
||||
11.1 CAUSE EXTERIEURE
|
||||
|
||||
Aucune des Parties ne sera responsable d'un retard ou d'une d<>faillance
|
||||
d'ex<65>cution du Contrat qui serait d<> <20> un cas de force majeure, un cas
|
||||
fortuit ou une cause ext<78>rieure, telle que, notamment, le mauvais
|
||||
fonctionnement ou les interruptions du r<>seau <20>lectrique ou de
|
||||
t<EFBFBD>l<EFBFBD>communication, la paralysie du r<>seau li<6C>e <20> une attaque
|
||||
informatique, l'intervention des autorit<69>s gouvernementales, les
|
||||
catastrophes naturelles, les d<>g<EFBFBD>ts des eaux, les tremblements de terre,
|
||||
le feu, les explosions, les gr<67>ves et les conflits sociaux, l'<27>tat de
|
||||
guerre...
|
||||
|
||||
11.2 Le fait, par l'une ou l'autre des Parties, d'omettre en une ou
|
||||
plusieurs occasions de se pr<70>valoir d'une ou plusieurs dispositions du
|
||||
Contrat, ne pourra en aucun cas impliquer renonciation par la Partie
|
||||
int<EFBFBD>ress<EFBFBD>e <20> s'en pr<70>valoir ult<6C>rieurement.
|
||||
|
||||
11.3 Le Contrat annule et remplace toute convention ant<6E>rieure, <20>crite
|
||||
ou orale, entre les Parties sur le m<>me objet et constitue l'accord
|
||||
entier entre les Parties sur cet objet. Aucune addition ou modification
|
||||
aux termes du Contrat n'aura d'effet <20> l'<27>gard des Parties <20> moins
|
||||
d'<27>tre faite par <20>crit et sign<67>e par leurs repr<70>sentants d<>ment habilit<69>s.
|
||||
|
||||
11.4 Dans l'hypoth<74>se o<> une ou plusieurs des dispositions du Contrat
|
||||
s'av<61>rerait contraire <20> une loi ou <20> un texte applicable, existants ou
|
||||
futurs, cette loi ou ce texte pr<70>vaudrait, et les Parties feraient les
|
||||
amendements n<>cessaires pour se conformer <20> cette loi ou <20> ce texte.
|
||||
Toutes les autres dispositions resteront en vigueur. De m<>me, la
|
||||
nullit<EFBFBD>, pour quelque raison que ce soit, d'une des dispositions du
|
||||
Contrat ne saurait entra<72>ner la nullit<69> de l'ensemble du Contrat.
|
||||
|
||||
|
||||
11.5 LANGUE
|
||||
|
||||
Le Contrat est r<>dig<69> en langue fran<61>aise et en langue anglaise, ces
|
||||
deux versions faisant <20>galement foi.
|
||||
|
||||
|
||||
Article 12 - NOUVELLES VERSIONS DU CONTRAT
|
||||
|
||||
12.1 Toute personne est autoris<69>e <20> copier et distribuer des copies de
|
||||
ce Contrat.
|
||||
|
||||
12.2 Afin d'en pr<70>server la coh<6F>rence, le texte du Contrat est prot<6F>g<EFBFBD>
|
||||
et ne peut <20>tre modifi<66> que par les auteurs de la licence, lesquels se
|
||||
r<EFBFBD>servent le droit de publier p<>riodiquement des mises <20> jour ou de
|
||||
nouvelles versions du Contrat, qui poss<73>deront chacune un num<75>ro
|
||||
distinct. Ces versions ult<6C>rieures seront susceptibles de prendre en
|
||||
compte de nouvelles probl<62>matiques rencontr<74>es par les logiciels libres.
|
||||
|
||||
12.3 Tout Logiciel diffus<75> sous une version donn<6E>e du Contrat ne pourra
|
||||
faire l'objet d'une diffusion ult<6C>rieure que sous la m<>me version du
|
||||
Contrat ou une version post<73>rieure, sous r<>serve des dispositions de
|
||||
l'article 5.3.4.
|
||||
|
||||
|
||||
Article 13 - LOI APPLICABLE ET COMPETENCE TERRITORIALE
|
||||
|
||||
13.1 Le Contrat est r<>gi par la loi fran<61>aise. Les Parties conviennent
|
||||
de tenter de r<>gler <20> l'amiable les diff<66>rends ou litiges qui
|
||||
viendraient <20> se produire par suite ou <20> l'occasion du Contrat.
|
||||
|
||||
13.2 A d<>faut d'accord amiable dans un d<>lai de deux (2) mois <20> compter
|
||||
de leur survenance et sauf situation relevant d'une proc<6F>dure d'urgence,
|
||||
les diff<66>rends ou litiges seront port<72>s par la Partie la plus diligente
|
||||
devant les Tribunaux comp<6D>tents de Paris.
|
||||
|
||||
|
||||
Version 2.0 du 2006-09-05.
|
||||
0
MANIFEST.in
Executable file → Normal file
0
MANIFEST.in
Executable file → Normal file
0
c-sandbox/obicount/Makefile
Executable file → Normal file
0
c-sandbox/obicount/Makefile
Executable file → Normal file
0
c-sandbox/obicount/obicount.c
Executable file → Normal file
0
c-sandbox/obicount/obicount.c
Executable file → Normal file
0
python/obitools3/dms/capi/__init__.py → distutils.ext/obidistutils/__init__.py
Executable file → Normal file
0
python/obitools3/dms/capi/__init__.py → distutils.ext/obidistutils/__init__.py
Executable file → Normal file
0
python/obitools3/format/__init__.py → distutils.ext/obidistutils/command/__init__.py
Executable file → Normal file
0
python/obitools3/format/__init__.py → distutils.ext/obidistutils/command/__init__.py
Executable file → Normal file
38
distutils.ext/obidistutils/command/build.py
Normal file
38
distutils.ext/obidistutils/command/build.py
Normal file
@ -0,0 +1,38 @@
|
||||
'''
|
||||
Created on 20 oct. 2012
|
||||
|
||||
@author: coissac
|
||||
'''
|
||||
|
||||
from distutils.command.build import build as ori_build
|
||||
from obidistutils.serenity.checksystem import is_mac_system
|
||||
|
||||
|
||||
class build(ori_build):
|
||||
|
||||
def has_ext_modules(self):
|
||||
return self.distribution.has_ext_modules()
|
||||
|
||||
def has_pidname(self):
|
||||
return is_mac_system()
|
||||
|
||||
def has_doc(self):
|
||||
return True
|
||||
|
||||
def has_littlebigman(self):
|
||||
return True
|
||||
|
||||
try:
|
||||
from obidistutils.command.build_sphinx import build_sphinx # @UnusedImport
|
||||
|
||||
sub_commands = [("littlebigman",has_littlebigman),
|
||||
('pidname',has_pidname)
|
||||
] \
|
||||
+ ori_build.sub_commands + \
|
||||
[('build_sphinx',has_doc)]
|
||||
except ImportError:
|
||||
sub_commands = [("littlebigman",has_littlebigman),
|
||||
('pidname',has_pidname)
|
||||
] \
|
||||
+ ori_build.sub_commands
|
||||
|
||||
85
distutils.ext/obidistutils/command/build_cexe.py
Normal file
85
distutils.ext/obidistutils/command/build_cexe.py
Normal file
@ -0,0 +1,85 @@
|
||||
'''
|
||||
Created on 20 oct. 2012
|
||||
|
||||
@author: coissac
|
||||
'''
|
||||
|
||||
from .build_ctools import build_ctools
|
||||
from .build_exe import build_exe
|
||||
from distutils.errors import DistutilsSetupError
|
||||
from distutils import log
|
||||
import os
|
||||
|
||||
class build_cexe(build_ctools):
|
||||
|
||||
description = "build C/C++ executable distributed with Python extensions"
|
||||
|
||||
|
||||
def initialize_options(self):
|
||||
build_ctools.initialize_options(self)
|
||||
self.built_files = None
|
||||
|
||||
|
||||
def finalize_options(self):
|
||||
# This might be confusing: both build-cexe and build-temp default
|
||||
# to build-temp as defined by the "build" command. This is because
|
||||
# I think that C libraries are really just temporary build
|
||||
# by-products, at least from the point of view of building Python
|
||||
# extensions -- but I want to keep my options open.
|
||||
|
||||
build_cexe_dir = self.build_cexe
|
||||
build_ctools.finalize_options(self)
|
||||
|
||||
if build_cexe_dir is None:
|
||||
self.build_cexe=None
|
||||
|
||||
self.set_undefined_options('build',
|
||||
('build_scripts', 'build_cexe'))
|
||||
|
||||
self.set_undefined_options('build_files',
|
||||
('files', 'built_files'))
|
||||
|
||||
self.executables = self.distribution.executables
|
||||
# self.build_cexe = os.path.join(os.path.dirname(self.build_cexe),'cbinaries')
|
||||
# self.mkpath(self.build_cexe)
|
||||
|
||||
if self.executables:
|
||||
self.check_executable_list(self.executables)
|
||||
|
||||
|
||||
# XXX same as for build_ext -- what about 'self.define' and
|
||||
# 'self.undef' ?
|
||||
|
||||
def substitute_sources(self,exe_name,sources):
|
||||
"""
|
||||
Substitutes source file name starting by an @ by the actual
|
||||
name of the built file (see --> build_files)
|
||||
"""
|
||||
sources = list(sources)
|
||||
for i in range(len(sources)):
|
||||
message = "%s :-> %s" % (exe_name,sources[i])
|
||||
if sources[i][0]=='@':
|
||||
try:
|
||||
filename = self.built_files[sources[i][1:]]
|
||||
except KeyError:
|
||||
raise DistutilsSetupError(
|
||||
'The %s filename declared in the source '
|
||||
'files of the program %s have not been '
|
||||
'built by the installation process' % (sources[i],
|
||||
exe_name))
|
||||
sources[i]=filename
|
||||
log.info("%s changed to %s",message,filename)
|
||||
else:
|
||||
log.info("%s ok",message)
|
||||
|
||||
return sources
|
||||
|
||||
def run(self):
|
||||
|
||||
for cmd_name in self.get_sub_commands():
|
||||
self.run_command(cmd_name)
|
||||
|
||||
build_exe.run(self)
|
||||
|
||||
|
||||
|
||||
63
distutils.ext/obidistutils/command/build_ctools.py
Normal file
63
distutils.ext/obidistutils/command/build_ctools.py
Normal file
@ -0,0 +1,63 @@
|
||||
'''
|
||||
Created on 20 oct. 2012
|
||||
|
||||
@author: coissac
|
||||
'''
|
||||
|
||||
|
||||
from .build_exe import build_exe
|
||||
from distutils import log
|
||||
|
||||
class build_ctools(build_exe):
|
||||
description = "build C/C++ executable not distributed with Python extensions"
|
||||
|
||||
def initialize_options(self):
|
||||
build_exe.initialize_options(self)
|
||||
|
||||
# List of built tools
|
||||
self.ctools = None
|
||||
self.littlebigman = None
|
||||
|
||||
|
||||
def finalize_options(self):
|
||||
# This might be confusing: both build-cexe and build-temp default
|
||||
# to build-temp as defined by the "build" command. This is because
|
||||
# I think that C libraries are really just temporary build
|
||||
# by-products, at least from the point of view of building Python
|
||||
# extensions -- but I want to keep my options open.
|
||||
|
||||
build_exe.finalize_options(self)
|
||||
|
||||
|
||||
self.set_undefined_options('build',
|
||||
('build_temp', 'build_cexe'))
|
||||
|
||||
self.set_undefined_options('littlebigman',
|
||||
('littlebigman', 'littlebigman'))
|
||||
|
||||
self.executables = self.distribution.ctools
|
||||
self.check_executable_list(self.executables)
|
||||
|
||||
|
||||
if self.littlebigman =='-DLITTLE_END':
|
||||
if self.define is None:
|
||||
self.define=[('LITTLE_END',None)]
|
||||
else:
|
||||
self.define.append('LITTLE_END',None)
|
||||
|
||||
log.info('Look for CPU architecture... %s',self.define)
|
||||
|
||||
self.ctools = set()
|
||||
|
||||
def run(self):
|
||||
|
||||
for cmd_name in self.get_sub_commands():
|
||||
self.run_command(cmd_name)
|
||||
|
||||
|
||||
build_exe.run(self)
|
||||
|
||||
for e,p in self.executables: # @UnusedVariable
|
||||
self.ctools.add(e)
|
||||
|
||||
|
||||
211
distutils.ext/obidistutils/command/build_exe.py
Normal file
211
distutils.ext/obidistutils/command/build_exe.py
Normal file
@ -0,0 +1,211 @@
|
||||
'''
|
||||
Created on 20 oct. 2012
|
||||
|
||||
@author: coissac
|
||||
'''
|
||||
|
||||
import os
|
||||
|
||||
from distutils.core import Command
|
||||
from distutils.sysconfig import customize_compiler
|
||||
from distutils.errors import DistutilsSetupError
|
||||
from distutils import log
|
||||
from distutils.ccompiler import show_compilers
|
||||
|
||||
class build_exe(Command):
|
||||
|
||||
description = "build an executable -- Abstract command "
|
||||
|
||||
user_options = [
|
||||
('build-cexe', 'x',
|
||||
"directory to build C/C++ libraries to"),
|
||||
('build-temp', 't',
|
||||
"directory to put temporary build by-products"),
|
||||
('debug', 'g',
|
||||
"compile with debugging information"),
|
||||
('force', 'f',
|
||||
"forcibly build everything (ignore file timestamps)"),
|
||||
('compiler=', 'c',
|
||||
"specify the compiler type"),
|
||||
]
|
||||
|
||||
boolean_options = ['debug', 'force']
|
||||
|
||||
help_options = [
|
||||
('help-compiler', None,
|
||||
"list available compilers", show_compilers),
|
||||
]
|
||||
|
||||
def initialize_options(self):
|
||||
self.build_cexe = None
|
||||
self.build_temp = None
|
||||
|
||||
# List of executables to build
|
||||
self.executables = None
|
||||
|
||||
# Compilation options for all libraries
|
||||
self.include_dirs = None
|
||||
self.define = None
|
||||
self.undef = None
|
||||
self.extra_compile_args = None
|
||||
self.debug = None
|
||||
self.force = 0
|
||||
self.compiler = None
|
||||
self.sse = None
|
||||
self.built_files=None
|
||||
|
||||
def finalize_options(self):
|
||||
# This might be confusing: both build-cexe and build-temp default
|
||||
# to build-temp as defined by the "build" command. This is because
|
||||
# I think that C libraries are really just temporary build
|
||||
# by-products, at least from the point of view of building Python
|
||||
# extensions -- but I want to keep my options open.
|
||||
self.set_undefined_options('build',
|
||||
('build_temp', 'build_temp'),
|
||||
('compiler', 'compiler'),
|
||||
('debug', 'debug'),
|
||||
('force', 'force'))
|
||||
|
||||
if self.include_dirs is None:
|
||||
self.include_dirs = self.distribution.include_dirs or []
|
||||
|
||||
if isinstance(self.include_dirs, str):
|
||||
self.include_dirs = self.include_dirs.split(os.pathsep)
|
||||
|
||||
self.sse = self.distribution.sse
|
||||
|
||||
if self.sse is not None:
|
||||
if self.extra_compile_args is None:
|
||||
self.extra_compile_args=['-m%s' % self.sse]
|
||||
else:
|
||||
self.extra_compile_args.append('-m%s' % self.sse)
|
||||
|
||||
# XXX same as for build_ext -- what about 'self.define' and
|
||||
# 'self.undef' ?
|
||||
|
||||
def run(self):
|
||||
|
||||
if not self.executables:
|
||||
return
|
||||
|
||||
self.mkpath(self.build_cexe)
|
||||
|
||||
# Yech -- this is cut 'n pasted from build_ext.py!
|
||||
from distutils.ccompiler import new_compiler
|
||||
self.compiler = new_compiler(compiler=self.compiler,
|
||||
dry_run=self.dry_run,
|
||||
force=self.force)
|
||||
customize_compiler(self.compiler)
|
||||
|
||||
if self.include_dirs is not None:
|
||||
self.compiler.set_include_dirs(self.include_dirs)
|
||||
if self.define is not None:
|
||||
# 'define' option is a list of (name,value) tuples
|
||||
for (name,value) in self.define:
|
||||
self.compiler.define_macro(name, value)
|
||||
|
||||
if self.undef is not None:
|
||||
for macro in self.undef:
|
||||
self.compiler.undefine_macro(macro)
|
||||
|
||||
self.build_executables(self.executables)
|
||||
|
||||
|
||||
def check_executable_list(self, executables):
|
||||
"""Ensure that the list of executables is valid.
|
||||
|
||||
`executable` is presumably provided as a command option 'executables'.
|
||||
This method checks that it is a list of 2-tuples, where the tuples
|
||||
are (executable_name, build_info_dict).
|
||||
|
||||
Raise DistutilsSetupError if the structure is invalid anywhere;
|
||||
just returns otherwise.
|
||||
"""
|
||||
if not isinstance(executables, list):
|
||||
raise DistutilsSetupError("'executables' option must be a list of tuples")
|
||||
|
||||
for exe in executables:
|
||||
if not isinstance(exe, tuple) and len(exe) != 2:
|
||||
raise DistutilsSetupError("each element of 'executables' must a 2-tuple")
|
||||
|
||||
name, build_info = exe
|
||||
|
||||
if not isinstance(name, str):
|
||||
raise DistutilsSetupError(
|
||||
"first element of each tuple in 'executables' "
|
||||
"must be a string (the executables name)")
|
||||
|
||||
if '/' in name or (os.sep != '/' and os.sep in name):
|
||||
raise DistutilsSetupError(
|
||||
"bad executable name '%s': "
|
||||
"may not contain directory separators" % exe[0])
|
||||
|
||||
if not isinstance(build_info, dict):
|
||||
raise DistutilsSetupError(
|
||||
"second element of each tuple in 'executables' "
|
||||
"must be a dictionary (build info)")
|
||||
|
||||
def get_executable_names(self):
|
||||
# Assume the executables list is valid -- 'check_executable_list()' is
|
||||
# called from 'finalize_options()', so it should be!
|
||||
if not self.executables:
|
||||
return None
|
||||
|
||||
exe_names = []
|
||||
for (exe_name, build_info) in self.executables: # @UnusedVariable
|
||||
exe_names.append(exe_name)
|
||||
return exe_names
|
||||
|
||||
|
||||
def get_source_files(self):
|
||||
self.check_executable_list(self.executables)
|
||||
filenames = []
|
||||
for (exe_name, build_info) in self.executables: # @UnusedVariable
|
||||
sources = build_info.get('sources')
|
||||
if sources is None or not isinstance(sources, (list, tuple)):
|
||||
raise DistutilsSetupError(
|
||||
"in 'executables' option (library '%s'), "
|
||||
"'sources' must be present and must be "
|
||||
"a list of source filenames" % exe_name)
|
||||
|
||||
filenames.extend(sources)
|
||||
return filenames
|
||||
|
||||
def substitute_sources(self,exe_name,sources):
|
||||
return list(sources)
|
||||
|
||||
def build_executables(self, executables):
|
||||
for (exe_name, build_info) in executables:
|
||||
sources = build_info.get('sources')
|
||||
if sources is None or not isinstance(sources, (list, tuple)):
|
||||
raise DistutilsSetupError(
|
||||
"in 'executables' option (library '%s'), "
|
||||
"'sources' must be present and must be "
|
||||
"a list of source filenames" % exe_name)
|
||||
|
||||
sources = self.substitute_sources(exe_name,sources)
|
||||
|
||||
log.info("building '%s' program", exe_name)
|
||||
|
||||
# First, compile the source code to object files in the library
|
||||
# directory. (This should probably change to putting object
|
||||
# files in a temporary build directory.)
|
||||
macros = build_info.get('macros')
|
||||
include_dirs = build_info.get('include_dirs')
|
||||
extra_args = self.extra_compile_args or []
|
||||
|
||||
objects = self.compiler.compile(sources,
|
||||
output_dir=self.build_temp,
|
||||
macros=macros,
|
||||
include_dirs=include_dirs,
|
||||
extra_postargs=extra_args,
|
||||
debug=self.debug)
|
||||
|
||||
# Now "link" the object files together into a static library.
|
||||
# (On Unix at least, this isn't really linking -- it just
|
||||
# builds an archive. Whatever.)
|
||||
self.compiler.link_executable(objects, exe_name,
|
||||
output_dir=self.build_cexe,
|
||||
debug=self.debug)
|
||||
|
||||
|
||||
115
distutils.ext/obidistutils/command/build_ext.py
Normal file
115
distutils.ext/obidistutils/command/build_ext.py
Normal file
@ -0,0 +1,115 @@
|
||||
'''
|
||||
Created on 13 fevr. 2014
|
||||
|
||||
@author: coissac
|
||||
'''
|
||||
|
||||
from distutils import log
|
||||
import os
|
||||
|
||||
|
||||
from distutils.errors import DistutilsSetupError
|
||||
|
||||
try:
|
||||
from Cython.Distutils import build_ext as ori_build_ext # @UnresolvedImport
|
||||
from Cython.Compiler import Options as cython_options # @UnresolvedImport
|
||||
class build_ext(ori_build_ext):
|
||||
|
||||
|
||||
def modifyDocScripts(self):
|
||||
build_dir_file=open("doc/sphinx/build_dir.txt","w")
|
||||
print(self.build_lib,file=build_dir_file)
|
||||
build_dir_file.close()
|
||||
|
||||
def initialize_options(self):
|
||||
ori_build_ext.initialize_options(self) # @UndefinedVariable
|
||||
self.littlebigman = None
|
||||
self.built_files = None
|
||||
|
||||
|
||||
def finalize_options(self):
|
||||
ori_build_ext.finalize_options(self) # @UndefinedVariable
|
||||
|
||||
self.set_undefined_options('littlebigman',
|
||||
('littlebigman', 'littlebigman'))
|
||||
|
||||
self.set_undefined_options('build_files',
|
||||
('files', 'built_files'))
|
||||
|
||||
self.cython_c_in_temp = 1
|
||||
|
||||
if self.littlebigman =='-DLITTLE_END':
|
||||
if self.define is None:
|
||||
self.define=[('LITTLE_END',None)]
|
||||
else:
|
||||
self.define.append('LITTLE_END',None)
|
||||
|
||||
def substitute_sources(self,exe_name,sources):
|
||||
"""
|
||||
Substitutes source file name starting by an @ by the actual
|
||||
name of the built file (see --> build_files)
|
||||
"""
|
||||
sources = list(sources)
|
||||
for i in range(len(sources)):
|
||||
message = "%s :-> %s" % (exe_name,sources[i])
|
||||
if sources[i][0]=='@':
|
||||
try:
|
||||
filename = self.built_files[sources[i][1:]]
|
||||
except KeyError:
|
||||
tmpfilename = os.path.join(self.build_temp,sources[i][1:])
|
||||
if os.path.isfile (tmpfilename):
|
||||
filename = tmpfilename
|
||||
else:
|
||||
raise DistutilsSetupError(
|
||||
'The %s filename declared in the source '
|
||||
'files of the program %s have not been '
|
||||
'built by the installation process' % (sources[i],
|
||||
exe_name))
|
||||
sources[i]=filename
|
||||
log.info("%s changed to %s",message,filename)
|
||||
else:
|
||||
log.info("%s ok",message)
|
||||
|
||||
return sources
|
||||
|
||||
def build_extensions(self):
|
||||
# First, sanity-check the 'extensions' list
|
||||
|
||||
for ext in self.extensions:
|
||||
ext.sources = self.substitute_sources(ext.name,ext.sources)
|
||||
|
||||
self.check_extensions_list(self.extensions)
|
||||
|
||||
for ext in self.extensions:
|
||||
log.info("%s :-> %s",ext.name,ext.sources)
|
||||
ext.sources = self.cython_sources(ext.sources, ext)
|
||||
self.build_extension(ext)
|
||||
|
||||
|
||||
def run(self):
|
||||
self.modifyDocScripts()
|
||||
|
||||
for cmd_name in self.get_sub_commands():
|
||||
self.run_command(cmd_name)
|
||||
|
||||
cython_options.annotate = True
|
||||
ori_build_ext.run(self) # @UndefinedVariable
|
||||
|
||||
|
||||
def has_files(self):
|
||||
return self.distribution.has_files()
|
||||
|
||||
def has_executables(self):
|
||||
return self.distribution.has_executables()
|
||||
|
||||
sub_commands = [('build_files',has_files),
|
||||
('build_cexe', has_executables)
|
||||
] + \
|
||||
ori_build_ext.sub_commands
|
||||
|
||||
except ImportError:
|
||||
from distutils.command import build_ext # @UnusedImport
|
||||
|
||||
|
||||
|
||||
|
||||
63
distutils.ext/obidistutils/command/build_files.py
Normal file
63
distutils.ext/obidistutils/command/build_files.py
Normal file
@ -0,0 +1,63 @@
|
||||
'''
|
||||
Created on 20 oct. 2012
|
||||
|
||||
@author: coissac
|
||||
'''
|
||||
|
||||
import os.path
|
||||
|
||||
from distutils.core import Command
|
||||
from distutils import log
|
||||
|
||||
class build_files(Command):
|
||||
|
||||
def initialize_options(self):
|
||||
self.files=None
|
||||
self.ctools=None
|
||||
self.build_temp=None
|
||||
self.build_cexe=None
|
||||
|
||||
def finalize_options(self):
|
||||
|
||||
self.set_undefined_options('build_ctools',
|
||||
('ctools', 'ctools'),
|
||||
('build_temp','build_temp'),
|
||||
('build_cexe','build_cexe'),
|
||||
)
|
||||
|
||||
self.files = {}
|
||||
|
||||
def run(self):
|
||||
|
||||
for cmd_name in self.get_sub_commands():
|
||||
self.run_command(cmd_name)
|
||||
|
||||
|
||||
for dest,prog,command in self.distribution.files:
|
||||
destfile = os.path.join(self.build_temp,dest)
|
||||
if prog in self.ctools:
|
||||
progfile = os.path.join(self.build_cexe,prog)
|
||||
else:
|
||||
progfile = prog
|
||||
|
||||
log.info("Building file : %s" % dest)
|
||||
|
||||
commandline = command % {'prog' : progfile,
|
||||
'dest' : destfile}
|
||||
|
||||
log.info(" --> %s" % commandline)
|
||||
|
||||
os.system(commandline)
|
||||
self.files[dest]=destfile
|
||||
|
||||
log.info("Done.\n")
|
||||
|
||||
def has_ctools(self):
|
||||
return self.distribution.has_ctools()
|
||||
|
||||
|
||||
sub_commands = [('build_ctools', has_ctools)] + \
|
||||
Command.sub_commands
|
||||
|
||||
|
||||
|
||||
104
distutils.ext/obidistutils/command/build_scripts.py
Normal file
104
distutils.ext/obidistutils/command/build_scripts.py
Normal file
@ -0,0 +1,104 @@
|
||||
'''
|
||||
Created on 20 oct. 2012
|
||||
|
||||
@author: coissac
|
||||
'''
|
||||
|
||||
import os.path
|
||||
|
||||
from distutils.command.build_scripts import build_scripts as ori_build_scripts
|
||||
from distutils.util import convert_path
|
||||
from distutils import log, sysconfig
|
||||
from distutils.dep_util import newer
|
||||
from stat import ST_MODE
|
||||
import re
|
||||
|
||||
first_line_re = re.compile('^#!.*python[0-9.]*([ \t].*)?$')
|
||||
|
||||
class build_scripts(ori_build_scripts):
|
||||
|
||||
def copy_scripts (self):
|
||||
"""Copy each script listed in 'self.scripts'; if it's marked as a
|
||||
Python script in the Unix way (first line matches 'first_line_re',
|
||||
ie. starts with "\#!" and contains "python"), then adjust the first
|
||||
line to refer to the current Python interpreter as we copy.
|
||||
"""
|
||||
self.mkpath(self.build_dir)
|
||||
rawbuild_dir = os.path.join(os.path.dirname(self.build_dir),'raw_scripts')
|
||||
self.mkpath(rawbuild_dir)
|
||||
|
||||
outfiles = []
|
||||
for script in self.scripts:
|
||||
adjust = 0
|
||||
script = convert_path(script)
|
||||
outfile = os.path.join(self.build_dir, os.path.splitext(os.path.basename(script))[0])
|
||||
rawoutfile = os.path.join(rawbuild_dir, os.path.basename(script))
|
||||
outfiles.append(outfile)
|
||||
|
||||
if not self.force and not newer(script, outfile):
|
||||
log.debug("not copying %s (up-to-date)", script)
|
||||
continue
|
||||
|
||||
# Always open the file but ignore failures in dry-run mode --
|
||||
# that way, we'll get accurate feedback if we can read the
|
||||
# script.
|
||||
try:
|
||||
f = open(script, "r")
|
||||
except IOError:
|
||||
if not self.dry_run:
|
||||
raise
|
||||
f = None
|
||||
else:
|
||||
first_line = f.readline()
|
||||
if not first_line:
|
||||
self.warn("%s is an empty file (skipping)" % script)
|
||||
continue
|
||||
|
||||
match = first_line_re.match(first_line)
|
||||
if match:
|
||||
adjust = 1
|
||||
post_interp = match.group(1) or ''
|
||||
|
||||
log.info("Store the raw script %s -> %s", script,rawoutfile)
|
||||
self.copy_file(script, rawoutfile)
|
||||
|
||||
|
||||
if adjust:
|
||||
log.info("copying and adjusting %s -> %s", script,
|
||||
self.build_dir)
|
||||
if not self.dry_run:
|
||||
outf = open(outfile, "w")
|
||||
if not sysconfig.python_build:
|
||||
outf.write("#!%s%s\n" %
|
||||
(self.executable,
|
||||
post_interp))
|
||||
else:
|
||||
outf.write("#!%s%s\n" %
|
||||
(os.path.join(
|
||||
sysconfig.get_config_var("BINDIR"),
|
||||
"python%s%s" % (sysconfig.get_config_var("VERSION"),
|
||||
sysconfig.get_config_var("EXE"))),
|
||||
post_interp))
|
||||
outf.writelines(f.readlines())
|
||||
outf.close()
|
||||
if f:
|
||||
f.close()
|
||||
else:
|
||||
if f:
|
||||
f.close()
|
||||
self.copy_file(script, outfile)
|
||||
|
||||
if os.name == 'posix':
|
||||
for F in outfiles:
|
||||
if self.dry_run:
|
||||
log.info("changing mode of %s", F)
|
||||
else:
|
||||
oldmode = os.stat(F)[ST_MODE]
|
||||
oldmode = oldmode & 0o7777
|
||||
|
||||
newmode = (oldmode | 0o555) & 0o7777
|
||||
if newmode != oldmode:
|
||||
log.info("changing mode of %s from %o to %o",
|
||||
F, oldmode, newmode)
|
||||
os.chmod(F, newmode)
|
||||
|
||||
27
distutils.ext/obidistutils/command/build_sphinx.py
Normal file
27
distutils.ext/obidistutils/command/build_sphinx.py
Normal file
@ -0,0 +1,27 @@
|
||||
'''
|
||||
Created on 10 mars 2015
|
||||
|
||||
@author: coissac
|
||||
'''
|
||||
|
||||
try:
|
||||
from sphinx.setup_command import BuildDoc as ori_build_sphinx # @UnresolvedImport
|
||||
|
||||
class build_sphinx(ori_build_sphinx):
|
||||
'''Build Sphinx documentation in html, epub and man formats
|
||||
'''
|
||||
|
||||
description = __doc__
|
||||
|
||||
def run(self):
|
||||
self.builder='html'
|
||||
self.finalize_options()
|
||||
ori_build_sphinx.run(self)
|
||||
self.builder='epub'
|
||||
self.finalize_options()
|
||||
ori_build_sphinx.run(self)
|
||||
self.builder='man'
|
||||
self.finalize_options()
|
||||
ori_build_sphinx.run(self)
|
||||
except ImportError:
|
||||
pass
|
||||
19
distutils.ext/obidistutils/command/install.py
Normal file
19
distutils.ext/obidistutils/command/install.py
Normal file
@ -0,0 +1,19 @@
|
||||
'''
|
||||
Created on 6 oct. 2014
|
||||
|
||||
@author: coissac
|
||||
'''
|
||||
|
||||
# try:
|
||||
# from setuptools.command.install import install as install_ori
|
||||
# except ImportError:
|
||||
# from distutils.command.install import install as install_ori
|
||||
|
||||
from distutils.command.install import install as install_ori
|
||||
|
||||
class install(install_ori):
|
||||
|
||||
def __init__(self,dist):
|
||||
install_ori.__init__(self, dist)
|
||||
# self.sub_commands.insert(0, ('build',lambda self: True))
|
||||
self.sub_commands.append(('install_sphinx',lambda self: self.distribution.serenity))
|
||||
47
distutils.ext/obidistutils/command/install_scripts.py
Normal file
47
distutils.ext/obidistutils/command/install_scripts.py
Normal file
@ -0,0 +1,47 @@
|
||||
'''
|
||||
Created on 20 oct. 2012
|
||||
|
||||
@author: coissac
|
||||
'''
|
||||
|
||||
# try:
|
||||
# from setuptools.command.install_scripts import install_scripts as ori_install_scripts
|
||||
# except ImportError:
|
||||
# from distutils.command.install_scripts import install_scripts as ori_install_scripts
|
||||
|
||||
from distutils.command.install_scripts import install_scripts as ori_install_scripts
|
||||
|
||||
import os.path
|
||||
from distutils import log
|
||||
|
||||
class install_scripts(ori_install_scripts):
|
||||
|
||||
def initialize_options(self):
|
||||
ori_install_scripts.initialize_options(self)
|
||||
self.public_dir = None
|
||||
|
||||
|
||||
def install_public_link(self):
|
||||
self.mkpath(self.public_dir)
|
||||
for file in self.get_outputs():
|
||||
log.info("exporting file %s -> %s", file,os.path.join(self.public_dir,
|
||||
os.path.split(file)[1]
|
||||
))
|
||||
if not self.dry_run:
|
||||
dest = os.path.join(self.public_dir,
|
||||
os.path.split(file)[1]
|
||||
)
|
||||
if os.path.exists(dest):
|
||||
os.unlink(dest)
|
||||
os.symlink(file,dest)
|
||||
|
||||
|
||||
|
||||
def run(self):
|
||||
ori_install_scripts.run(self)
|
||||
if self.distribution.serenity:
|
||||
self.public_dir=os.path.join(self.install_dir,"../export/bin")
|
||||
self.public_dir=os.path.abspath(self.public_dir)
|
||||
self.install_public_link()
|
||||
|
||||
|
||||
61
distutils.ext/obidistutils/command/install_sphinx.py
Normal file
61
distutils.ext/obidistutils/command/install_sphinx.py
Normal file
@ -0,0 +1,61 @@
|
||||
'''
|
||||
Created on 10 mars 2015
|
||||
|
||||
@author: coissac
|
||||
'''
|
||||
from distutils.core import Command
|
||||
import os.path
|
||||
import glob
|
||||
|
||||
class install_sphinx(Command):
|
||||
'''
|
||||
Install the sphinx documentation
|
||||
'''
|
||||
|
||||
description = "Install the sphinx documentation in serenity mode"
|
||||
|
||||
boolean_options = ['force', 'skip-build']
|
||||
|
||||
|
||||
def initialize_options (self):
|
||||
self.install_doc = None
|
||||
self.build_dir = None
|
||||
|
||||
def finalize_options (self):
|
||||
self.set_undefined_options('build_sphinx', ('build_dir', 'build_dir'))
|
||||
self.set_undefined_options('install',
|
||||
('install_scripts', 'install_doc'))
|
||||
|
||||
def run (self):
|
||||
if self.distribution.serenity:
|
||||
self.install_doc = os.path.join(self.install_doc,"../export/share")
|
||||
self.install_doc=os.path.abspath(self.install_doc)
|
||||
self.mkpath(self.install_doc)
|
||||
self.mkpath(os.path.join(self.install_doc,'html'))
|
||||
outfiles = self.copy_tree(os.path.join(self.build_dir,'html'), # @UnusedVariable
|
||||
os.path.join(self.install_doc,'html'))
|
||||
|
||||
self.mkpath(os.path.join(self.install_doc,'man','man1'))
|
||||
outfiles = self.copy_tree(os.path.join(self.build_dir,'man'), # @UnusedVariable
|
||||
os.path.join(self.install_doc,'man','man1'))
|
||||
|
||||
for epub in glob.glob(os.path.join(self.build_dir,'epub/*.epub')):
|
||||
self.copy_file(os.path.join(epub),
|
||||
os.path.join(self.install_doc,os.path.split(epub)[1]))
|
||||
|
||||
def get_outputs(self):
|
||||
directory=os.path.join(self.install_doc,'html')
|
||||
files = [os.path.join(self.install_doc,'html', f)
|
||||
for dp, dn, filenames in os.walk(directory) for f in filenames] # @UnusedVariable
|
||||
|
||||
directory=os.path.join(self.build_dir,'man')
|
||||
files.append(os.path.join(self.install_doc,'man','man1', f)
|
||||
for dp, dn, filenames in os.walk(directory) for f in filenames) # @UnusedVariable
|
||||
|
||||
directory=os.path.join(self.build_dir,'epub')
|
||||
files.append(os.path.join(self.install_doc, f)
|
||||
for dp, dn, filenames in os.walk(directory) # @UnusedVariable
|
||||
for f in glob.glob(os.path.join(dp, '*.epub')) )
|
||||
|
||||
return files
|
||||
|
||||
59
distutils.ext/obidistutils/command/littlebigman.py
Normal file
59
distutils.ext/obidistutils/command/littlebigman.py
Normal file
@ -0,0 +1,59 @@
|
||||
'''
|
||||
Created on 20 oct. 2012
|
||||
|
||||
@author: coissac
|
||||
'''
|
||||
|
||||
import os
|
||||
|
||||
from obidistutils.command.build_exe import build_exe
|
||||
from distutils import log
|
||||
|
||||
import subprocess
|
||||
|
||||
class littlebigman(build_exe):
|
||||
|
||||
description = "build the littlebigman executable testing endianness of the CPU"
|
||||
|
||||
|
||||
def initialize_options(self):
|
||||
build_exe.initialize_options(self)
|
||||
|
||||
self.littlebigman = None
|
||||
|
||||
|
||||
def finalize_options(self):
|
||||
# This might be confusing: both build-cexe and build-temp default
|
||||
# to build-temp as defined by the "build" command. This is because
|
||||
# I think that C libraries are really just temporary build
|
||||
# by-products, at least from the point of view of building Python
|
||||
# extensions -- but I want to keep my options open.
|
||||
|
||||
build_exe.finalize_options(self)
|
||||
|
||||
self.set_undefined_options('build',
|
||||
('build_temp', 'build_cexe'))
|
||||
|
||||
# self.ctools = self.distribution.ctools
|
||||
|
||||
if os.path.isfile("distutils.ext/src/littlebigman.c"):
|
||||
self.executables = [('littlebigman',{"sources":["distutils.ext/src/littlebigman.c"]})]
|
||||
self.check_executable_list(self.executables)
|
||||
else:
|
||||
self.executables = []
|
||||
|
||||
|
||||
def run_littlebigman(self):
|
||||
p = subprocess.Popen("'%s'" % os.path.join(self.build_temp,
|
||||
'littlebigman'),
|
||||
shell=True,
|
||||
stdout=subprocess.PIPE)
|
||||
little = p.communicate()[0]
|
||||
return little.decode('latin1')
|
||||
|
||||
def run(self):
|
||||
build_exe.run(self)
|
||||
self.littlebigman=self.run_littlebigman()
|
||||
log.info("Your CPU is in mode : %s" % self.littlebigman)
|
||||
|
||||
|
||||
55
distutils.ext/obidistutils/command/pidname.py
Normal file
55
distutils.ext/obidistutils/command/pidname.py
Normal file
@ -0,0 +1,55 @@
|
||||
'''
|
||||
Created on 20 oct. 2012
|
||||
|
||||
@author: coissac
|
||||
'''
|
||||
|
||||
import os
|
||||
|
||||
from obidistutils.command.build_exe import build_exe
|
||||
from obidistutils.serenity.checksystem import is_mac_system
|
||||
|
||||
|
||||
class pidname(build_exe):
|
||||
|
||||
description = "build the pidname executable returning the executable path from a PID on a mac"
|
||||
|
||||
|
||||
def initialize_options(self):
|
||||
build_exe.initialize_options(self)
|
||||
|
||||
self.pidname = False
|
||||
|
||||
|
||||
def finalize_options(self):
|
||||
# This might be confusing: both build-cexe and build-temp default
|
||||
# to build-temp as defined by the "build" command. This is because
|
||||
# I think that C libraries are really just temporary build
|
||||
# by-products, at least from the point of view of building Python
|
||||
# extensions -- but I want to keep my options open.
|
||||
|
||||
build_exe.finalize_options(self)
|
||||
|
||||
self.set_undefined_options('build',
|
||||
('build_scripts', 'build_cexe'))
|
||||
|
||||
# self.ctools = self.distribution.ctools
|
||||
|
||||
if os.path.isfile("distutils.ext/src/pidname.c"):
|
||||
self.executables = [('pidname',{"sources":["distutils.ext/src/pidname.c"]})]
|
||||
self.check_executable_list(self.executables)
|
||||
else:
|
||||
self.executables = []
|
||||
|
||||
# self.build_cexe = os.path.join(os.path.dirname(self.build_cexe),'cbinaries')
|
||||
# self.mkpath(self.build_cexe)
|
||||
|
||||
|
||||
|
||||
def run(self):
|
||||
if is_mac_system():
|
||||
build_exe.run(self)
|
||||
self.pidname=True
|
||||
else:
|
||||
self.pidname=False
|
||||
|
||||
42
distutils.ext/obidistutils/command/sdist.py
Normal file
42
distutils.ext/obidistutils/command/sdist.py
Normal file
@ -0,0 +1,42 @@
|
||||
'''
|
||||
Created on 10 mars 2015
|
||||
|
||||
@author: coissac
|
||||
'''
|
||||
|
||||
import os.path
|
||||
|
||||
from distutils.command.sdist import sdist as orig_sdist
|
||||
from distutils import dir_util
|
||||
|
||||
class sdist(orig_sdist):
|
||||
|
||||
def make_distribution(self):
|
||||
"""Create the source distribution(s). First, we create the release
|
||||
tree with 'make_release_tree()'; then, we create all required
|
||||
archive files (according to 'self.formats') from the release tree.
|
||||
Finally, we clean up by blowing away the release tree (unless
|
||||
'self.keep_temp' is true). The list of archive files created is
|
||||
stored so it can be retrieved later by 'get_archive_files()'.
|
||||
"""
|
||||
# Don't warn about missing meta-data here -- should be (and is!)
|
||||
# done elsewhere.
|
||||
base_dir = self.distribution.get_fullname()
|
||||
base_name = os.path.join(self.dist_dir,base_dir)
|
||||
|
||||
self.make_release_tree(os.path.join('tmp',base_dir), self.filelist.files)
|
||||
archive_files = [] # remember names of files we create
|
||||
# tar archive must be created last to avoid overwrite and remove
|
||||
if 'tar' in self.formats:
|
||||
self.formats.append(self.formats.pop(self.formats.index('tar')))
|
||||
|
||||
for fmt in self.formats:
|
||||
file = self.make_archive(base_name, fmt, root_dir='tmp',base_dir=base_dir,
|
||||
owner=self.owner, group=self.group)
|
||||
archive_files.append(file)
|
||||
self.distribution.dist_files.append(('sdist', '', file))
|
||||
|
||||
self.archive_files = archive_files
|
||||
|
||||
if not self.keep_temp:
|
||||
dir_util.remove_tree(os.path.join('tmp',base_dir), dry_run=self.dry_run)
|
||||
226
distutils.ext/obidistutils/core.py
Normal file
226
distutils.ext/obidistutils/core.py
Normal file
@ -0,0 +1,226 @@
|
||||
'''
|
||||
Created on 20 oct. 2012
|
||||
|
||||
@author: coissac
|
||||
'''
|
||||
|
||||
from os import path
|
||||
import os.path
|
||||
import glob
|
||||
import sys
|
||||
|
||||
# try:
|
||||
# from setuptools.extension import Extension
|
||||
# except ImportError:
|
||||
# from distutils.extension import Extension
|
||||
|
||||
from distutils.extension import Extension
|
||||
|
||||
from obidistutils.serenity.checkpackage import install_requirements,\
|
||||
check_requirements, \
|
||||
RequirementError
|
||||
|
||||
from obidistutils.serenity.rerun import enforce_good_python
|
||||
from obidistutils.serenity.rerun import rerun_with_anothe_python
|
||||
from distutils import log
|
||||
|
||||
from obidistutils.dist import Distribution
|
||||
from obidistutils.serenity import is_serenity
|
||||
|
||||
|
||||
def findPackage(root,base=None):
|
||||
modules=[]
|
||||
if base is None:
|
||||
base=[]
|
||||
for module in (path.basename(path.dirname(x))
|
||||
for x in glob.glob(path.join(root,'*','__init__.py'))):
|
||||
modules.append('.'.join(base+[module]))
|
||||
modules.extend(findPackage(path.join(root,module),base+[module]))
|
||||
return modules
|
||||
|
||||
def findCython(root,base=None,pyrexs=None):
|
||||
setupdir = os.path.dirname(sys.argv[0])
|
||||
pyrexs=[]
|
||||
|
||||
if base is None:
|
||||
base=[]
|
||||
for module in (path.basename(path.dirname(x))
|
||||
for x in glob.glob(path.join(root,'*','__init__.py'))):
|
||||
|
||||
|
||||
for pyrex in glob.glob(path.join(root,module,'*.pyx')):
|
||||
pyrexs.append(Extension('.'.join(base+[module,path.splitext(path.basename(pyrex))[0]]),
|
||||
[pyrex]
|
||||
)
|
||||
)
|
||||
try:
|
||||
cfiles = os.path.splitext(pyrex)[0]+".cfiles"
|
||||
cfilesdir = os.path.dirname(cfiles)
|
||||
cfiles = open(cfiles)
|
||||
cfiles = [os.path.relpath(os.path.join(cfilesdir,y),setupdir).strip()
|
||||
if y[0] !='@' else y.strip()
|
||||
for y in cfiles]
|
||||
|
||||
log.info("Cython module : %s",cfiles)
|
||||
incdir = set(os.path.dirname(x) for x in cfiles if x[-2:]==".h")
|
||||
cfiles = [x for x in cfiles if x[-2:]==".c"]
|
||||
pyrexs[-1].sources.extend(cfiles)
|
||||
pyrexs[-1].include_dirs.extend(incdir)
|
||||
pyrexs[-1].extra_compile_args.extend(['-msse2',
|
||||
'-Wno-unused-function',
|
||||
'-Wmissing-braces',
|
||||
'-Wchar-subscripts'])
|
||||
|
||||
except IOError:
|
||||
pass
|
||||
|
||||
pyrexs.extend(findCython(path.join(root,module),base+[module]))
|
||||
return pyrexs
|
||||
|
||||
|
||||
def rootname(x):
|
||||
return os.path.splitext(x.sources[0])[0]
|
||||
|
||||
|
||||
def prepare_commands():
|
||||
from obidistutils.command.build import build
|
||||
from obidistutils.command.littlebigman import littlebigman
|
||||
# from obidistutils.command.serenity import serenity
|
||||
from obidistutils.command.build_cexe import build_cexe
|
||||
from obidistutils.command.build_ext import build_ext
|
||||
from obidistutils.command.build_ctools import build_ctools
|
||||
from obidistutils.command.build_files import build_files
|
||||
from obidistutils.command.build_scripts import build_scripts
|
||||
from obidistutils.command.install_scripts import install_scripts
|
||||
from obidistutils.command.install_sphinx import install_sphinx
|
||||
from obidistutils.command.install import install
|
||||
from obidistutils.command.pidname import pidname
|
||||
from obidistutils.command.sdist import sdist
|
||||
|
||||
|
||||
|
||||
COMMANDS = {'build':build,
|
||||
# 'serenity':serenity,
|
||||
'littlebigman':littlebigman,
|
||||
'pidname':pidname,
|
||||
'build_ctools':build_ctools,
|
||||
'build_files':build_files,
|
||||
'build_cexe':build_cexe,
|
||||
'build_ext': build_ext,
|
||||
'build_scripts':build_scripts,
|
||||
'install_scripts':install_scripts,
|
||||
'install_sphinx':install_sphinx,
|
||||
'install':install,
|
||||
'sdist':sdist}
|
||||
|
||||
# try:
|
||||
# from setuptools.commands import egg_info
|
||||
# COMMANDS['egg_info']=egg_info
|
||||
# except ImportError:
|
||||
# pass
|
||||
try:
|
||||
from obidistutils.command.build_sphinx import build_sphinx
|
||||
COMMANDS['build_sphinx']=build_sphinx
|
||||
except ImportError:
|
||||
pass
|
||||
|
||||
return COMMANDS
|
||||
|
||||
|
||||
CTOOLS =[]
|
||||
CEXES =[]
|
||||
FILES =[]
|
||||
|
||||
def setup(**attrs):
|
||||
|
||||
log.set_threshold(log.INFO)
|
||||
|
||||
minversion = attrs.get("pythonmin",'3.4')
|
||||
maxversion = attrs.get('pythonmax',None)
|
||||
fork = attrs.get('fork',False)
|
||||
requirementfile = attrs.get('requirements','requirements.txt')
|
||||
|
||||
try:
|
||||
del attrs['pythonmin']
|
||||
except KeyError:
|
||||
pass
|
||||
|
||||
try:
|
||||
del attrs['pythonmax']
|
||||
except KeyError:
|
||||
pass
|
||||
|
||||
try:
|
||||
del attrs['fork']
|
||||
except KeyError:
|
||||
pass
|
||||
|
||||
try:
|
||||
del attrs['requirements']
|
||||
except KeyError:
|
||||
pass
|
||||
|
||||
if is_serenity():
|
||||
|
||||
|
||||
enforce_good_python(minversion, maxversion, fork)
|
||||
|
||||
if (install_requirements(requirementfile)):
|
||||
rerun_with_anothe_python(sys.executable,minversion,maxversion,fork)
|
||||
|
||||
|
||||
try:
|
||||
check_requirements(requirementfile)
|
||||
except RequirementError as e :
|
||||
log.error(e)
|
||||
sys.exit(1)
|
||||
|
||||
if 'distclass' not in attrs:
|
||||
attrs['distclass']=Distribution
|
||||
|
||||
if 'python_src' not in attrs:
|
||||
SRC = 'python'
|
||||
else:
|
||||
SRC = attrs['python_src']
|
||||
del(attrs['python_src'])
|
||||
|
||||
if 'scripts' not in attrs:
|
||||
attrs['scripts'] = glob.glob('%s/*.py' % SRC)
|
||||
|
||||
if 'package_dir' not in attrs:
|
||||
attrs['package_dir'] = {'': SRC}
|
||||
|
||||
if 'packages' not in attrs:
|
||||
attrs['packages'] = findPackage(SRC)
|
||||
|
||||
if 'cmdclass' not in attrs:
|
||||
attrs['cmdclass'] = prepare_commands()
|
||||
|
||||
if 'ctools' not in attrs:
|
||||
attrs['ctools'] = CTOOLS
|
||||
|
||||
if 'executables' not in attrs:
|
||||
attrs['executables'] = CEXES
|
||||
|
||||
if 'files' not in attrs:
|
||||
attrs['files'] = FILES
|
||||
|
||||
if 'sse' not in attrs:
|
||||
attrs['sse']=None
|
||||
|
||||
if 'serenity' not in attrs:
|
||||
attrs['serenity']=False
|
||||
|
||||
EXTENTION=findCython(SRC)
|
||||
|
||||
if 'ext_modules' not in attrs:
|
||||
attrs['ext_modules'] = EXTENTION
|
||||
|
||||
# try:
|
||||
# from setuptools.core import setup as ori_setup
|
||||
# except ImportError:
|
||||
# from distutils.core import setup as ori_setup
|
||||
|
||||
from distutils.core import setup as ori_setup
|
||||
|
||||
ori_setup(**attrs)
|
||||
58
distutils.ext/obidistutils/dist.py
Normal file
58
distutils.ext/obidistutils/dist.py
Normal file
@ -0,0 +1,58 @@
|
||||
'''
|
||||
Created on 20 oct. 2012
|
||||
|
||||
@author: coissac
|
||||
'''
|
||||
|
||||
# try:
|
||||
# from setuptools.dist import Distribution as ori_Distribution
|
||||
# except ImportError:
|
||||
# from distutils.dist import Distribution as ori_Distribution
|
||||
|
||||
from distutils.dist import Distribution as ori_Distribution
|
||||
|
||||
class Distribution(ori_Distribution):
|
||||
|
||||
def __init__(self,attrs=None):
|
||||
self.executables = None
|
||||
self.ctools = None
|
||||
self.files = None
|
||||
self.build_cexe = None
|
||||
self.deprecated_scripts = None
|
||||
self.zip_safe=False
|
||||
self.sse = None
|
||||
self.serenity=attrs['serenity']
|
||||
|
||||
ori_Distribution.__init__(self, attrs)
|
||||
|
||||
self.global_options.insert(0,('serenity', None, "install or build the package in a python virtualenv "
|
||||
"without polluting the installed python and with many "
|
||||
"checks during the installation process"
|
||||
))
|
||||
self.global_options.insert(0,('virtualenv', None, "if the installation is done using the serenity mode "
|
||||
"this option allows for specifying the virtualenv name. "
|
||||
"By default the name is PACKAGE-VERSION"
|
||||
))
|
||||
|
||||
def run_commands(self):
|
||||
"""Run each command that was seen on the setup script command line.
|
||||
Uses the list of commands found and cache of command objects
|
||||
created by 'get_command_obj()'.
|
||||
"""
|
||||
# self.run_command('littlebigman')
|
||||
ori_Distribution.run_commands(self)
|
||||
|
||||
|
||||
def has_executables(self):
|
||||
return self.executables is not None and self.executables
|
||||
|
||||
def has_ctools(self):
|
||||
return self.ctools is not None and self.ctools
|
||||
|
||||
def has_files(self):
|
||||
return self.files is not None and self.files
|
||||
|
||||
def has_deprecated_scripts(self):
|
||||
return self.deprecated_scripts is not None and self.deprecated_scripts
|
||||
|
||||
|
||||
112
distutils.ext/obidistutils/serenity/__init__.py
Normal file
112
distutils.ext/obidistutils/serenity/__init__.py
Normal file
@ -0,0 +1,112 @@
|
||||
import sys
|
||||
|
||||
from distutils import util
|
||||
from distutils import sysconfig
|
||||
from distutils import log
|
||||
from distutils.version import LooseVersion, StrictVersion
|
||||
import glob
|
||||
import os
|
||||
import subprocess
|
||||
import re
|
||||
from distutils.errors import DistutilsError
|
||||
import tempfile
|
||||
|
||||
from importlib.util import spec_from_file_location # @UnresolvedImport
|
||||
import zipimport
|
||||
|
||||
import argparse
|
||||
|
||||
import base64
|
||||
|
||||
from .checkpython import is_python_version
|
||||
|
||||
|
||||
from obidistutils.serenity.rerun import enforce_good_python
|
||||
from obidistutils.serenity.rerun import rerun_with_anothe_python
|
||||
|
||||
from obidistutils.serenity.virtual import serenity_virtualenv
|
||||
|
||||
from obidistutils.serenity.checksystem import is_mac_system, \
|
||||
is_windows_system
|
||||
|
||||
from obidistutils.serenity.checkpackage import install_requirements
|
||||
from obidistutils.serenity.checkpackage import check_requirements
|
||||
|
||||
from obidistutils.serenity.util import save_argv
|
||||
|
||||
from obidistutils.serenity.snake import snake
|
||||
|
||||
|
||||
def serenity_snake(envname,package,version):
|
||||
old = log.set_threshold(log.INFO)
|
||||
|
||||
log.info("Installing %s (%s) in serenity mode" % (package,version))
|
||||
|
||||
enforce_good_python()
|
||||
|
||||
virtualpython=serenity_virtualenv(envname,package,version)
|
||||
|
||||
if virtualpython!=os.path.realpath(sys.executable):
|
||||
log.info("Restarting installation within the %s virtualenv" % (envname))
|
||||
rerun_with_anothe_python(virtualpython)
|
||||
|
||||
log.info("%s will be installed with python : %s" % (package,virtualpython))
|
||||
|
||||
if install_requirements():
|
||||
log.info("Restarting installation with all dependencies ok")
|
||||
rerun_with_anothe_python(virtualpython)
|
||||
|
||||
log.set_threshold(old)
|
||||
|
||||
def serenity_assert(version):
|
||||
check_requirements()
|
||||
|
||||
|
||||
def is_serenity():
|
||||
from obidistutils.serenity.globals import local_serenity
|
||||
return local_serenity and local_serenity[0]
|
||||
|
||||
def serenity_mode(package,version):
|
||||
|
||||
save_argv()
|
||||
|
||||
|
||||
from obidistutils.serenity.globals import saved_args
|
||||
from obidistutils.serenity.globals import local_serenity
|
||||
|
||||
|
||||
old = log.set_threshold(log.INFO)
|
||||
|
||||
argparser = argparse.ArgumentParser(add_help=False)
|
||||
argparser.add_argument('--serenity',
|
||||
dest='serenity',
|
||||
action='store_true',
|
||||
default=False,
|
||||
help='Switch the installer in serenity mode. Everythings are installed in a virtualenv')
|
||||
|
||||
argparser.add_argument('--virtualenv',
|
||||
dest='virtual',
|
||||
type=str,
|
||||
action='store',
|
||||
default="%s-%s" % (package,version),
|
||||
help='Specify the name of the virtualenv used by the serenity mode [default: %s-%s]' % (package,version))
|
||||
|
||||
args, unknown = argparser.parse_known_args()
|
||||
sys.argv = [sys.argv[0]] + unknown
|
||||
|
||||
if args.serenity:
|
||||
local_serenity.append(True)
|
||||
serenity_snake(args.virtual,package,version)
|
||||
else:
|
||||
local_serenity.append(False)
|
||||
|
||||
log.set_threshold(old)
|
||||
|
||||
return args.serenity
|
||||
|
||||
|
||||
def getVersion(source,main,version):
|
||||
path = os.path.join(source,main,'%s.py' % version)
|
||||
spec = spec_from_file_location('version',path)
|
||||
return spec.loader.load_module().version.strip()
|
||||
|
||||
36
distutils.ext/obidistutils/serenity/bootstrappip.py
Normal file
36
distutils.ext/obidistutils/serenity/bootstrappip.py
Normal file
@ -0,0 +1,36 @@
|
||||
'''
|
||||
Created on 22 janv. 2016
|
||||
|
||||
@author: coissac
|
||||
'''
|
||||
|
||||
import sys
|
||||
from urllib import request
|
||||
import os.path
|
||||
|
||||
from obidistutils.serenity.util import get_serenity_dir
|
||||
from obidistutils.serenity.rerun import rerun_with_anothe_python
|
||||
from obidistutils.serenity.checkpython import is_a_virtualenv_python
|
||||
|
||||
getpipurl="https://bootstrap.pypa.io/get-pip.py"
|
||||
|
||||
def bootstrap():
|
||||
|
||||
getpipfile=os.path.join(get_serenity_dir(),"get-pip.py")
|
||||
|
||||
with request.urlopen(getpipurl) as getpip:
|
||||
with open(getpipfile,"wb") as out:
|
||||
for l in getpip:
|
||||
out.write(l)
|
||||
|
||||
python = sys.executable
|
||||
|
||||
if is_a_virtualenv_python():
|
||||
command= "%s %s" % (python,getpipfile)
|
||||
else:
|
||||
command= "%s %s --user" % (python,getpipfile)
|
||||
|
||||
os.system(command)
|
||||
|
||||
rerun_with_anothe_python(python)
|
||||
|
||||
165
distutils.ext/obidistutils/serenity/checkpackage.py
Normal file
165
distutils.ext/obidistutils/serenity/checkpackage.py
Normal file
@ -0,0 +1,165 @@
|
||||
'''
|
||||
Created on 2 oct. 2014
|
||||
|
||||
@author: coissac
|
||||
'''
|
||||
|
||||
import re
|
||||
import os
|
||||
|
||||
try:
|
||||
import pip # @UnresolvedImport
|
||||
from pip.utils import get_installed_distributions # @UnresolvedImport
|
||||
except ImportError:
|
||||
from .bootstrappip import bootstrap
|
||||
bootstrap()
|
||||
|
||||
from distutils.version import StrictVersion # @UnusedImport
|
||||
from distutils.errors import DistutilsError
|
||||
from distutils import log
|
||||
|
||||
class RequirementError(Exception):
|
||||
pass
|
||||
|
||||
def is_installed(requirement):
|
||||
|
||||
|
||||
requirement_project,requirement_relation,requirement_version = parse_package_requirement(requirement)
|
||||
|
||||
package = [x for x in get_installed_distributions() if x.project_name==requirement_project]
|
||||
|
||||
if len(package)==1:
|
||||
if requirement_version is not None and requirement_relation is not None:
|
||||
rep = (len(package)==1) and eval("StrictVersion('%s') %s StrictVersion('%s')" % (package[0].version,
|
||||
requirement_relation,
|
||||
requirement_version)
|
||||
)
|
||||
else:
|
||||
rep=True
|
||||
else:
|
||||
rep=False
|
||||
|
||||
if rep:
|
||||
if requirement_version is not None and requirement_relation is not None:
|
||||
log.info("Look for package %s (%s%s) : ok version %s installed" % (requirement_project,
|
||||
requirement_relation,
|
||||
requirement_version,
|
||||
package[0].version))
|
||||
else:
|
||||
log.info("Look for package %s : ok version %s installed" % (requirement_project,
|
||||
package[0].version))
|
||||
else:
|
||||
if len(package)!=1:
|
||||
log.info("Look for package %s (%s%s) : not installed" % (requirement_project,
|
||||
requirement_relation,
|
||||
requirement_version))
|
||||
else:
|
||||
log.info("Look for package %s (%s%s) : failed only version %s installed" % (requirement_project,
|
||||
requirement_relation,
|
||||
requirement_version,
|
||||
package[0].version))
|
||||
|
||||
return rep
|
||||
|
||||
|
||||
def get_requirements(requirementfile='requirements.txt'):
|
||||
|
||||
try:
|
||||
requirements = open(requirementfile).readlines()
|
||||
requirements = [x.strip() for x in requirements]
|
||||
requirements = [x for x in requirements if x[0]!='-']
|
||||
|
||||
except IOError:
|
||||
requirements = []
|
||||
|
||||
return requirements
|
||||
|
||||
|
||||
def install_requirements(requirementfile='requirements.txt'):
|
||||
|
||||
install_something=False
|
||||
|
||||
requirements = get_requirements(requirementfile)
|
||||
|
||||
log.info("Required packages for the installation :")
|
||||
for x in requirements:
|
||||
ok = is_installed(x)
|
||||
if not ok:
|
||||
log.info(" Installing requirement : %s" % x)
|
||||
pip_install_package(x)
|
||||
install_something=True
|
||||
if x[0:3]=='pip':
|
||||
return True
|
||||
|
||||
return install_something
|
||||
|
||||
|
||||
def check_requirements(requirementfile='requirements.txt'):
|
||||
|
||||
requirements = get_requirements(requirementfile)
|
||||
|
||||
log.info("Required packages for the installation :")
|
||||
for x in requirements:
|
||||
ok = is_installed(x)
|
||||
if not ok:
|
||||
raise RequirementError(" Missing requirement : %s -- Package installation stopped" % x)
|
||||
|
||||
|
||||
|
||||
|
||||
def parse_package_requirement(requirement):
|
||||
|
||||
version_pattern = re.compile('[=><]+(.*)$')
|
||||
project_pattern = re.compile('[^=><]+')
|
||||
relationship_pattern = re.compile('[=><]+')
|
||||
|
||||
try:
|
||||
requirement_project = project_pattern.search(requirement).group(0)
|
||||
requirement_version = version_pattern.search(requirement)
|
||||
if requirement_version is not None:
|
||||
requirement_version=requirement_version.group(1)
|
||||
requirement_relation= relationship_pattern.search(requirement)
|
||||
if requirement_relation is not None:
|
||||
requirement_relation=requirement_relation.group(0)
|
||||
except:
|
||||
raise DistutilsError("Requirement : %s not correctly formated" % requirement)
|
||||
|
||||
return requirement_project,requirement_relation,requirement_version
|
||||
|
||||
|
||||
def get_package_requirement(package,requirementfile='requirements.txt'):
|
||||
requirements = get_requirements(requirementfile)
|
||||
req = [x for x in requirements
|
||||
if x[0:len(package)]==package
|
||||
]
|
||||
|
||||
if len(req)==1:
|
||||
return req[0]
|
||||
else:
|
||||
return None
|
||||
|
||||
|
||||
def pip_install_package(package,directory=None,upgrade=True):
|
||||
|
||||
if directory is not None:
|
||||
log.info(' installing %s in directory %s' % (package,str(directory)))
|
||||
|
||||
|
||||
if 'http_proxy' in os.environ and 'https_proxy' not in os.environ:
|
||||
os.environ['https_proxy']=os.environ['http_proxy']
|
||||
|
||||
args = ['install']
|
||||
|
||||
if upgrade:
|
||||
args.append('--upgrade')
|
||||
|
||||
if 'https_proxy' in os.environ:
|
||||
args.append('--proxy=%s' % os.environ['https_proxy'])
|
||||
|
||||
if directory is not None:
|
||||
args.append('--target=%s' % directory)
|
||||
|
||||
args.append(package)
|
||||
|
||||
return pip.main(args)
|
||||
|
||||
138
distutils.ext/obidistutils/serenity/checkpython.py
Normal file
138
distutils.ext/obidistutils/serenity/checkpython.py
Normal file
@ -0,0 +1,138 @@
|
||||
'''
|
||||
Created on 24 mai 2015
|
||||
|
||||
@author: coissac
|
||||
'''
|
||||
from distutils.version import StrictVersion
|
||||
from distutils import sysconfig
|
||||
import subprocess
|
||||
import os
|
||||
import glob
|
||||
import re
|
||||
|
||||
from obidistutils.serenity.checksystem import is_windows_system
|
||||
import sys
|
||||
|
||||
|
||||
def is_python_version(path=None,minversion='3.4',maxversion=None):
|
||||
'''
|
||||
Checks that the python version is in the range {minversion,maxversion[
|
||||
|
||||
@param path: if None consider the running python
|
||||
otherwise the python pointed by the path
|
||||
@param minversion: the minimum version to consider
|
||||
@param maxversion: the maximum version to consider (strictly inferior to)
|
||||
|
||||
@return: True if the python version match
|
||||
@rtype: bool
|
||||
'''
|
||||
if path is None:
|
||||
pythonversion = StrictVersion(sysconfig.get_python_version())
|
||||
else:
|
||||
command = """'%s' -c 'from distutils import sysconfig; """ \
|
||||
"""print(sysconfig.get_python_version())'""" % path
|
||||
|
||||
p = subprocess.Popen(command,
|
||||
shell=True,
|
||||
stdout=subprocess.PIPE)
|
||||
pythonversion=str(p.communicate()[0],'utf8').strip()
|
||||
pythonversion = StrictVersion(pythonversion)
|
||||
|
||||
return ( pythonversion >=StrictVersion(minversion)
|
||||
and ( maxversion is None
|
||||
or pythonversion < StrictVersion(maxversion))
|
||||
)
|
||||
|
||||
|
||||
def lookfor_good_python(minversion='3.4',maxversion=None,followLink=False):
|
||||
'''
|
||||
Look for all python interpreters present in the system path that
|
||||
match the version constraints.
|
||||
|
||||
@param minversion: the minimum version to consider
|
||||
@param maxversion: the maximum version to consider (strictly inferior to)
|
||||
@param followLink: a boolean value indicating if link must be substituted
|
||||
by their real path.
|
||||
|
||||
@return: a list of path to interpreters
|
||||
'''
|
||||
exe = []
|
||||
if not is_windows_system():
|
||||
paths = os.environ['PATH'].split(os.pathsep)
|
||||
for p in paths:
|
||||
candidates = glob.glob(os.path.join(p,'python*'))
|
||||
pexe = []
|
||||
pythonpat=re.compile('python([0-9]|[0-9]\.[0-9])?$')
|
||||
for e in candidates:
|
||||
print(e)
|
||||
if pythonpat.search(e) is not None:
|
||||
if followLink and os.path.islink(e):
|
||||
e = os.path.realpath(e)
|
||||
if (os.path.isfile(e) and
|
||||
os.access(e, os.X_OK) and
|
||||
is_python_version(e,minversion,maxversion)):
|
||||
pexe.append(e)
|
||||
exe.extend(set(pexe))
|
||||
|
||||
return exe
|
||||
|
||||
def is_a_virtualenv_python(path=None):
|
||||
'''
|
||||
Check if the python is belonging a virtualenv
|
||||
|
||||
@param path: the path pointing to the python executable.
|
||||
if path is None then the running python is
|
||||
considered.
|
||||
@param path: str or None
|
||||
|
||||
@return: True if the python belongs a virtualenv
|
||||
False otherwise
|
||||
@rtype: bool
|
||||
|
||||
'''
|
||||
if path is None:
|
||||
rep = sys.base_exec_prefix != sys.exec_prefix
|
||||
else:
|
||||
command = """'%s' -c 'import sys; print(sys.base_exec_prefix != sys.exec_prefix)'""" % path
|
||||
p = subprocess.Popen(command,
|
||||
shell=True,
|
||||
stdout=subprocess.PIPE)
|
||||
rep = eval(str(p.communicate()[0],'utf8'))
|
||||
|
||||
return rep
|
||||
|
||||
|
||||
def which_virtualenv(path=None,full=False):
|
||||
'''
|
||||
Returns the name of the virtualenv.
|
||||
@param path: the path to a python binary or None
|
||||
if you want to consider the running python
|
||||
@type path: str or None
|
||||
|
||||
@param full: if set to True, returns the absolute path,
|
||||
otherwise only return a simple directory name
|
||||
@type full: bool
|
||||
|
||||
@return: the virtual environment name or None if the
|
||||
path does not belong a virtualenv
|
||||
@rtype: str or None
|
||||
'''
|
||||
if path is None:
|
||||
path = sys.executable
|
||||
|
||||
if is_a_virtualenv_python(path):
|
||||
parts = path.split(os.sep)
|
||||
try:
|
||||
if full:
|
||||
rep = os.sep.join(parts[0:parts.index('bin')])
|
||||
rep = os.path.realpath(rep)
|
||||
else:
|
||||
rep = parts[parts.index('bin')-1]
|
||||
except ValueError:
|
||||
rep = None
|
||||
else:
|
||||
rep=None
|
||||
|
||||
return rep
|
||||
|
||||
|
||||
18
distutils.ext/obidistutils/serenity/checksystem.py
Normal file
18
distutils.ext/obidistutils/serenity/checksystem.py
Normal file
@ -0,0 +1,18 @@
|
||||
'''
|
||||
Created on 24 mai 2015
|
||||
|
||||
@author: coissac
|
||||
'''
|
||||
|
||||
from distutils import util
|
||||
|
||||
def is_mac_system():
|
||||
platform = util.get_platform().split('-')[0]
|
||||
|
||||
return platform=='macosx'
|
||||
|
||||
def is_windows_system():
|
||||
platform = util.get_platform().split('-')[0]
|
||||
|
||||
return platform=='Windows'
|
||||
|
||||
14
distutils.ext/obidistutils/serenity/globals.py
Normal file
14
distutils.ext/obidistutils/serenity/globals.py
Normal file
@ -0,0 +1,14 @@
|
||||
'''
|
||||
Created on 24 mai 2015
|
||||
|
||||
@author: coissac
|
||||
'''
|
||||
|
||||
|
||||
saved_args=[]
|
||||
tmpdir=[]
|
||||
local_pip=[]
|
||||
local_virtualenv=[]
|
||||
local_cython=[]
|
||||
local_serenity=[]
|
||||
|
||||
61
distutils.ext/obidistutils/serenity/rerun.py
Normal file
61
distutils.ext/obidistutils/serenity/rerun.py
Normal file
@ -0,0 +1,61 @@
|
||||
'''
|
||||
Created on 24 mai 2015
|
||||
|
||||
@author: coissac
|
||||
'''
|
||||
|
||||
import sys
|
||||
import os
|
||||
from distutils import log
|
||||
from distutils.errors import DistutilsError
|
||||
|
||||
|
||||
from obidistutils.serenity.globals import saved_args
|
||||
from obidistutils.serenity.checkpython import is_python_version,\
|
||||
lookfor_good_python
|
||||
|
||||
|
||||
def rerun_with_anothe_python(path, minversion='3.4',maxversion=None, fork=False):
|
||||
|
||||
if saved_args:
|
||||
args = saved_args
|
||||
else:
|
||||
args = list(sys.argv)
|
||||
|
||||
|
||||
assert is_python_version(path,minversion,maxversion), \
|
||||
'the selected python is not adapted to the installation of this package'
|
||||
|
||||
args.insert(0, path)
|
||||
|
||||
sys.stderr.flush()
|
||||
sys.stdout.flush()
|
||||
|
||||
if fork:
|
||||
log.info('Forking a new install process')
|
||||
os.system(' '.join(list(args)))
|
||||
log.info('External process ended')
|
||||
sys.exit(0)
|
||||
else:
|
||||
log.info('Install script restarting...')
|
||||
os.execv(path,list(args))
|
||||
|
||||
def enforce_good_python(minversion='3.4',maxversion=None, fork=False):
|
||||
if is_python_version(minversion=minversion,maxversion=maxversion):
|
||||
log.info('You are running the good python')
|
||||
return True
|
||||
|
||||
goodpython = lookfor_good_python(minversion,maxversion)
|
||||
|
||||
if not goodpython:
|
||||
raise DistutilsError('No good python identified on your system')
|
||||
|
||||
goodpython=goodpython[0]
|
||||
|
||||
log.warn("========================================")
|
||||
log.warn("")
|
||||
log.warn(" Switching to python : %s" % goodpython)
|
||||
log.warn("")
|
||||
log.warn("========================================")
|
||||
|
||||
rerun_with_anothe_python(goodpython)
|
||||
35
distutils.ext/obidistutils/serenity/snake.py
Normal file
35
distutils.ext/obidistutils/serenity/snake.py
Normal file
@ -0,0 +1,35 @@
|
||||
'''
|
||||
Created on 2 oct. 2014
|
||||
|
||||
@author: coissac
|
||||
'''
|
||||
|
||||
snake ="""
|
||||
|
||||
___
|
||||
,'._,`.
|
||||
(-.___.-)
|
||||
(-.___.-)
|
||||
`-.___.-'
|
||||
(( @ @| . __
|
||||
\ ` | ,\ |`. @| | | _.-._
|
||||
__`.`=-=mm===mm:: | | |`. | | | ,'=` '=`.
|
||||
( `-'|:/ /:/ `/ @| | | |, @| @| /---)W(---\
|
||||
\ \ / / / / @| | ' (----| |----) ,~
|
||||
|\ \ / /| / / @| \---| |---/ |
|
||||
| \ V /||/ / `.-| |-,' |
|
||||
| `-' |V / \| |/ @'
|
||||
| , |-' __| |__
|
||||
| .;: _,-. ,--""..| |..""--.
|
||||
;;:::' " ) (`--::__|_|__::--')
|
||||
,-" _, / \`--...___...--'/
|
||||
( -:--'/ / /`--...___...--'\
|
||||
"-._ `"'._/ /`---...___...---'\
|
||||
"-._ "---. (`---....___....---')
|
||||
.' ",._ ,' ) |`---....___....---'|
|
||||
/`._| `| | (`---....___....---')
|
||||
( \ | / \`---...___...---'/
|
||||
`. `, ^"" `:--...___...--;'
|
||||
`.,' hh `-._______.-'
|
||||
|
||||
"""
|
||||
27
distutils.ext/obidistutils/serenity/util.py
Normal file
27
distutils.ext/obidistutils/serenity/util.py
Normal file
@ -0,0 +1,27 @@
|
||||
'''
|
||||
Created on 2 oct. 2014
|
||||
|
||||
@author: coissac
|
||||
'''
|
||||
|
||||
import sys
|
||||
import tempfile
|
||||
|
||||
|
||||
from obidistutils.serenity.globals import tmpdir # @UnusedImport
|
||||
from obidistutils.serenity.globals import saved_args # @UnusedImport
|
||||
|
||||
def get_serenity_dir():
|
||||
global tmpdir
|
||||
|
||||
if not tmpdir:
|
||||
tmpdir.append(tempfile.mkdtemp())
|
||||
return tmpdir[0]
|
||||
|
||||
def save_argv():
|
||||
global saved_args
|
||||
|
||||
del saved_args[:]
|
||||
saved_args.extend(list(sys.argv))
|
||||
|
||||
|
||||
69
distutils.ext/obidistutils/serenity/virtual.py
Normal file
69
distutils.ext/obidistutils/serenity/virtual.py
Normal file
@ -0,0 +1,69 @@
|
||||
'''
|
||||
Created on 2 oct. 2014
|
||||
|
||||
@author: coissac
|
||||
'''
|
||||
|
||||
import os
|
||||
import sys
|
||||
import venv
|
||||
|
||||
from distutils.errors import DistutilsError
|
||||
from .globals import local_virtualenv # @UnusedImport
|
||||
from .checkpython import which_virtualenv,\
|
||||
is_python_version, \
|
||||
is_a_virtualenv_python
|
||||
|
||||
|
||||
|
||||
|
||||
def serenity_virtualenv(envname,package,version,minversion='3.4',maxversion=None):
|
||||
|
||||
#
|
||||
# Checks if we are already running under the good virtualenv
|
||||
#
|
||||
ve = which_virtualenv(full=True)
|
||||
if ve == os.path.realpath(envname) and is_python_version(minversion=minversion,maxversion=maxversion):
|
||||
return sys.executable
|
||||
|
||||
#
|
||||
# Check if the virtualenv exist
|
||||
#
|
||||
|
||||
python = None
|
||||
|
||||
if os.path.isdir(envname):
|
||||
python = os.path.join(envname,'bin','python')
|
||||
ok = (is_python_version(python,
|
||||
minversion=minversion,
|
||||
maxversion=maxversion) and
|
||||
is_a_virtualenv_python(python))
|
||||
|
||||
|
||||
#
|
||||
# The virtualenv already exist but it is not ok
|
||||
#
|
||||
if not ok:
|
||||
raise DistutilsError("A virtualenv %s already exists but not with the required python")
|
||||
|
||||
else:
|
||||
ok = False
|
||||
|
||||
|
||||
#
|
||||
# Creates a new virtualenv
|
||||
#
|
||||
if not ok:
|
||||
venv.create(envname,
|
||||
system_site_packages=False,
|
||||
clear=True,
|
||||
symlinks=False,
|
||||
with_pip=True)
|
||||
|
||||
# check the newly created virtualenv
|
||||
return serenity_virtualenv(envname,package,version)
|
||||
|
||||
return os.path.realpath(python)
|
||||
|
||||
|
||||
|
||||
24
distutils.ext/src/littlebigman.c
Normal file
24
distutils.ext/src/littlebigman.c
Normal file
@ -0,0 +1,24 @@
|
||||
/*
|
||||
* littlebigman.c
|
||||
*
|
||||
* Created on: 11 juil. 2012
|
||||
* Author: coissac
|
||||
*/
|
||||
|
||||
#include<stdio.h>
|
||||
|
||||
int main(int argc, char *argv[])
|
||||
{
|
||||
union { int entier;
|
||||
char caractere[4] ;
|
||||
} test;
|
||||
|
||||
test.entier=0x01020304;
|
||||
|
||||
if (test.caractere[3] == 1)
|
||||
printf("-DLITTLE_END");
|
||||
else
|
||||
printf("-DBIG_END");
|
||||
|
||||
return 0;
|
||||
}
|
||||
24
distutils.ext/src/pidname.c
Normal file
24
distutils.ext/src/pidname.c
Normal file
@ -0,0 +1,24 @@
|
||||
#include <stdio.h>
|
||||
#include <stdlib.h>
|
||||
#include <string.h>
|
||||
#include <errno.h>
|
||||
#include <libproc.h>
|
||||
|
||||
int main (int argc, char* argv[])
|
||||
{
|
||||
pid_t pid; int ret;
|
||||
char pathbuf[PROC_PIDPATHINFO_MAXSIZE];
|
||||
|
||||
if ( argc > 1 ) {
|
||||
pid = (pid_t) atoi(argv[1]);
|
||||
ret = proc_pidpath (pid, pathbuf, sizeof(pathbuf));
|
||||
if ( ret <= 0 ) {
|
||||
fprintf(stderr, "PID %d: proc_pidpath ();\n", pid);
|
||||
fprintf(stderr, " %s\n", strerror(errno));
|
||||
} else {
|
||||
printf("proc %d: %s\n", pid, pathbuf);
|
||||
}
|
||||
}
|
||||
|
||||
return 0;
|
||||
}
|
||||
0
doc/.gitignore
vendored
Executable file → Normal file
0
doc/.gitignore
vendored
Executable file → Normal file
0
doc/Doxyfile
Executable file → Normal file
0
doc/Doxyfile
Executable file → Normal file
0
doc/Makefile
Executable file → Normal file
0
doc/Makefile
Executable file → Normal file
8
doc/conf.py
Executable file → Normal file
8
doc/conf.py
Executable file → Normal file
@ -33,10 +33,10 @@ extensions = [
|
||||
'sphinx.ext.autodoc',
|
||||
'sphinx.ext.todo',
|
||||
'sphinx.ext.coverage',
|
||||
'sphinx.ext.imgmath',
|
||||
'sphinx.ext.pngmath',
|
||||
'sphinx.ext.ifconfig',
|
||||
'sphinx.ext.viewcode',
|
||||
'breathe',
|
||||
# 'breathe',
|
||||
]
|
||||
|
||||
# Add any paths that contain templates here, relative to this directory.
|
||||
@ -295,6 +295,4 @@ texinfo_documents = [
|
||||
sys.path.append( "breathe/" )
|
||||
breathe_projects = { "OBITools3": "doxygen/xml/" }
|
||||
breathe_default_project = "OBITools3"
|
||||
#breathe_projects_source = {
|
||||
# "auto" : ( "../src", ["obidms.h", "obiavl.h"] )
|
||||
# }
|
||||
|
||||
|
||||
0
doc/source/DMS.rst
Executable file → Normal file
0
doc/source/DMS.rst
Executable file → Normal file
0
doc/source/UML/OBIDMS_UML.png
Executable file → Normal file
0
doc/source/UML/OBIDMS_UML.png
Executable file → Normal file
|
Before Width: | Height: | Size: 67 KiB After Width: | Height: | Size: 67 KiB |
0
doc/source/UML/OBITypes_UML.class.violet.html
Executable file → Normal file
0
doc/source/UML/OBITypes_UML.class.violet.html
Executable file → Normal file
0
doc/source/UML/OBITypes_UML.png
Executable file → Normal file
0
doc/source/UML/OBITypes_UML.png
Executable file → Normal file
|
Before Width: | Height: | Size: 20 KiB After Width: | Height: | Size: 20 KiB |
0
doc/source/UML/ObiDMS_UML.class.violet.html
Executable file → Normal file
0
doc/source/UML/ObiDMS_UML.class.violet.html
Executable file → Normal file
0
doc/source/containers.rst
Executable file → Normal file
0
doc/source/containers.rst
Executable file → Normal file
0
doc/source/data.rst
Executable file → Normal file
0
doc/source/data.rst
Executable file → Normal file
0
doc/source/elementary.rst
Executable file → Normal file
0
doc/source/elementary.rst
Executable file → Normal file
0
doc/source/guidelines.rst
Executable file → Normal file
0
doc/source/guidelines.rst
Executable file → Normal file
0
doc/source/images/history.png
Executable file → Normal file
0
doc/source/images/history.png
Executable file → Normal file
|
Before Width: | Height: | Size: 17 KiB After Width: | Height: | Size: 17 KiB |
0
doc/source/images/version_control.png
Executable file → Normal file
0
doc/source/images/version_control.png
Executable file → Normal file
|
Before Width: | Height: | Size: 48 KiB After Width: | Height: | Size: 48 KiB |
2
doc/source/index.rst
Executable file → Normal file
2
doc/source/index.rst
Executable file → Normal file
@ -11,7 +11,7 @@ OBITools3 documentation
|
||||
|
||||
Programming guidelines <guidelines>
|
||||
Data structures <data>
|
||||
Code documentation <code_doc/codedoc>
|
||||
|
||||
|
||||
Indices and tables
|
||||
------------------
|
||||
|
||||
0
doc/source/specialvalues.rst
Executable file → Normal file
0
doc/source/specialvalues.rst
Executable file → Normal file
1
doc/source/types.rst
Executable file → Normal file
1
doc/source/types.rst
Executable file → Normal file
@ -4,7 +4,6 @@ OBITypes
|
||||
|
||||
|
||||
.. image:: ./UML/OBITypes_UML.png
|
||||
|
||||
:download:`html version of the OBITypes UML file <UML/OBITypes_UML.class.violet.html>`
|
||||
|
||||
|
||||
|
||||
2
doc/sphinx/.gitignore
vendored
2
doc/sphinx/.gitignore
vendored
@ -1,2 +0,0 @@
|
||||
.DS_Store
|
||||
/build_dir.txt
|
||||
1
doc/sphinx/build_dir.txt
Normal file
1
doc/sphinx/build_dir.txt
Normal file
@ -0,0 +1 @@
|
||||
build/lib.macosx-10.6-intel-3.5
|
||||
1
python/.gitignore
vendored
1
python/.gitignore
vendored
@ -1 +0,0 @@
|
||||
/OBITools3.egg-info/
|
||||
50
python/obi.py
Normal file
50
python/obi.py
Normal file
@ -0,0 +1,50 @@
|
||||
#!/usr/local/bin/python3.4
|
||||
'''
|
||||
obi -- shortdesc
|
||||
|
||||
obi is a description
|
||||
|
||||
It defines classes_and_methods
|
||||
|
||||
@author: user_name
|
||||
|
||||
@copyright: 2014 organization_name. All rights reserved.
|
||||
|
||||
@license: license
|
||||
|
||||
@contact: user_email
|
||||
@deffield updated: Updated
|
||||
'''
|
||||
|
||||
|
||||
default_config = { 'software' : "The OBITools",
|
||||
'log' : False,
|
||||
'loglevel' : 'INFO',
|
||||
'progress' : True,
|
||||
'defaultdms' : None
|
||||
}
|
||||
|
||||
root_config_name='obi'
|
||||
|
||||
from obitools3.apps.config import getConfiguration # @UnresolvedImport
|
||||
from obitools3.version import version
|
||||
|
||||
__all__ = []
|
||||
__version__ = version
|
||||
__date__ = '2014-09-28'
|
||||
__updated__ = '2014-09-28'
|
||||
|
||||
DEBUG = 1
|
||||
TESTRUN = 0
|
||||
PROFILE = 0
|
||||
|
||||
|
||||
if __name__ =="__main__":
|
||||
|
||||
config = getConfiguration(root_config_name,
|
||||
default_config)
|
||||
|
||||
config[root_config_name]['module'].run(config)
|
||||
|
||||
|
||||
|
||||
0
python/obitools3/__init__.py
Executable file → Normal file
0
python/obitools3/__init__.py
Executable file → Normal file
Binary file not shown.
0
python/obitools3/apps/__init__.py
Executable file → Normal file
0
python/obitools3/apps/__init__.py
Executable file → Normal file
@ -1,110 +0,0 @@
|
||||
../../../src/obi_lcs.h
|
||||
../../../src/obi_lcs.c
|
||||
../../../src/obierrno.h
|
||||
../../../src/obierrno.c
|
||||
../../../src/upperband.h
|
||||
../../../src/upperband.c
|
||||
../../../src/sse_banded_LCS_alignment.h
|
||||
../../../src/sse_banded_LCS_alignment.c
|
||||
../../../src/obiblob.h
|
||||
../../../src/obiblob.c
|
||||
../../../src/utils.h
|
||||
../../../src/utils.c
|
||||
../../../src/obidms.h
|
||||
../../../src/obidms.c
|
||||
../../../src/libjson/json_utils.h
|
||||
../../../src/libjson/json_utils.c
|
||||
../../../src/libjson/cJSON.h
|
||||
../../../src/libjson/cJSON.c
|
||||
../../../src/obiavl.h
|
||||
../../../src/obiavl.c
|
||||
../../../src/bloom.h
|
||||
../../../src/bloom.c
|
||||
../../../src/crc64.h
|
||||
../../../src/crc64.c
|
||||
../../../src/murmurhash2.h
|
||||
../../../src/murmurhash2.c
|
||||
../../../src/obidmscolumn.h
|
||||
../../../src/obidmscolumn.c
|
||||
../../../src/obitypes.h
|
||||
../../../src/obitypes.c
|
||||
../../../src/obidmscolumndir.h
|
||||
../../../src/obidmscolumndir.c
|
||||
../../../src/obiblob_indexer.h
|
||||
../../../src/obiblob_indexer.c
|
||||
../../../src/obiview.h
|
||||
../../../src/obiview.c
|
||||
../../../src/hashtable.h
|
||||
../../../src/hashtable.c
|
||||
../../../src/linked_list.h
|
||||
../../../src/linked_list.c
|
||||
../../../src/obidmscolumn_array.h
|
||||
../../../src/obidmscolumn_array.c
|
||||
../../../src/obidmscolumn_blob.h
|
||||
../../../src/obidmscolumn_blob.c
|
||||
../../../src/obidmscolumn_idx.h
|
||||
../../../src/obidmscolumn_idx.c
|
||||
../../../src/obidmscolumn_bool.h
|
||||
../../../src/obidmscolumn_bool.c
|
||||
../../../src/obidmscolumn_char.h
|
||||
../../../src/obidmscolumn_char.c
|
||||
../../../src/obidmscolumn_float.h
|
||||
../../../src/obidmscolumn_float.c
|
||||
../../../src/obidmscolumn_int.h
|
||||
../../../src/obidmscolumn_int.c
|
||||
../../../src/obidmscolumn_qual.h
|
||||
../../../src/obidmscolumn_qual.c
|
||||
../../../src/obidmscolumn_seq.h
|
||||
../../../src/obidmscolumn_seq.c
|
||||
../../../src/obidmscolumn_str.h
|
||||
../../../src/obidmscolumn_str.c
|
||||
../../../src/array_indexer.h
|
||||
../../../src/array_indexer.c
|
||||
../../../src/char_str_indexer.h
|
||||
../../../src/char_str_indexer.c
|
||||
../../../src/dna_seq_indexer.h
|
||||
../../../src/dna_seq_indexer.c
|
||||
../../../src/encode.c
|
||||
../../../src/encode.h
|
||||
../../../src/uint8_indexer.c
|
||||
../../../src/uint8_indexer.h
|
||||
../../../src/build_reference_db.c
|
||||
../../../src/build_reference_db.h
|
||||
../../../src/kmer_similarity.c
|
||||
../../../src/kmer_similarity.h
|
||||
../../../src/obi_clean.c
|
||||
../../../src/obi_clean.h
|
||||
../../../src/obi_ecopcr.c
|
||||
../../../src/obi_ecopcr.h
|
||||
../../../src/obi_ecotag.c
|
||||
../../../src/obi_ecotag.h
|
||||
../../../src/obidms_taxonomy.c
|
||||
../../../src/obidms_taxonomy.h
|
||||
../../../src/obilittlebigman.c
|
||||
../../../src/obilittlebigman.h
|
||||
../../../src/_sse.h
|
||||
../../../src/obidebug.h
|
||||
../../../src/libecoPCR/libapat/CODES/dft_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/dna_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/prot_code.h
|
||||
../../../src/libecoPCR/libapat/apat_parse.c
|
||||
../../../src/libecoPCR/libapat/apat_search.c
|
||||
../../../src/libecoPCR/libapat/apat.h
|
||||
../../../src/libecoPCR/libapat/Gmach.h
|
||||
../../../src/libecoPCR/libapat/Gtypes.h
|
||||
../../../src/libecoPCR/libapat/libstki.c
|
||||
../../../src/libecoPCR/libapat/libstki.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.c
|
||||
../../../src/libecoPCR/ecoapat.c
|
||||
../../../src/libecoPCR/ecodna.c
|
||||
../../../src/libecoPCR/ecoError.c
|
||||
../../../src/libecoPCR/ecoMalloc.c
|
||||
../../../src/libecoPCR/ecoPCR.h
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
0
python/obitools3/apps/arguments.pxd
Executable file → Normal file
0
python/obitools3/apps/arguments.pxd
Executable file → Normal file
3
python/obitools3/apps/arguments.pyx
Executable file → Normal file
3
python/obitools3/apps/arguments.pyx
Executable file → Normal file
@ -57,6 +57,5 @@ cpdef buildArgumentParser(str configname,
|
||||
module.addOptions(sub)
|
||||
|
||||
sub.set_defaults(**{'%s:module' % configname : module})
|
||||
sub.set_defaults(**{'%s:modulename' % configname : c})
|
||||
|
||||
|
||||
return parser
|
||||
|
||||
@ -1,110 +0,0 @@
|
||||
../../../src/obi_lcs.h
|
||||
../../../src/obi_lcs.c
|
||||
../../../src/obierrno.h
|
||||
../../../src/obierrno.c
|
||||
../../../src/upperband.h
|
||||
../../../src/upperband.c
|
||||
../../../src/sse_banded_LCS_alignment.h
|
||||
../../../src/sse_banded_LCS_alignment.c
|
||||
../../../src/obiblob.h
|
||||
../../../src/obiblob.c
|
||||
../../../src/utils.h
|
||||
../../../src/utils.c
|
||||
../../../src/obidms.h
|
||||
../../../src/obidms.c
|
||||
../../../src/libjson/json_utils.h
|
||||
../../../src/libjson/json_utils.c
|
||||
../../../src/libjson/cJSON.h
|
||||
../../../src/libjson/cJSON.c
|
||||
../../../src/obiavl.h
|
||||
../../../src/obiavl.c
|
||||
../../../src/bloom.h
|
||||
../../../src/bloom.c
|
||||
../../../src/crc64.h
|
||||
../../../src/crc64.c
|
||||
../../../src/murmurhash2.h
|
||||
../../../src/murmurhash2.c
|
||||
../../../src/obidmscolumn.h
|
||||
../../../src/obidmscolumn.c
|
||||
../../../src/obitypes.h
|
||||
../../../src/obitypes.c
|
||||
../../../src/obidmscolumndir.h
|
||||
../../../src/obidmscolumndir.c
|
||||
../../../src/obiblob_indexer.h
|
||||
../../../src/obiblob_indexer.c
|
||||
../../../src/obiview.h
|
||||
../../../src/obiview.c
|
||||
../../../src/hashtable.h
|
||||
../../../src/hashtable.c
|
||||
../../../src/linked_list.h
|
||||
../../../src/linked_list.c
|
||||
../../../src/obidmscolumn_array.h
|
||||
../../../src/obidmscolumn_array.c
|
||||
../../../src/obidmscolumn_blob.h
|
||||
../../../src/obidmscolumn_blob.c
|
||||
../../../src/obidmscolumn_idx.h
|
||||
../../../src/obidmscolumn_idx.c
|
||||
../../../src/obidmscolumn_bool.h
|
||||
../../../src/obidmscolumn_bool.c
|
||||
../../../src/obidmscolumn_char.h
|
||||
../../../src/obidmscolumn_char.c
|
||||
../../../src/obidmscolumn_float.h
|
||||
../../../src/obidmscolumn_float.c
|
||||
../../../src/obidmscolumn_int.h
|
||||
../../../src/obidmscolumn_int.c
|
||||
../../../src/obidmscolumn_qual.h
|
||||
../../../src/obidmscolumn_qual.c
|
||||
../../../src/obidmscolumn_seq.h
|
||||
../../../src/obidmscolumn_seq.c
|
||||
../../../src/obidmscolumn_str.h
|
||||
../../../src/obidmscolumn_str.c
|
||||
../../../src/array_indexer.h
|
||||
../../../src/array_indexer.c
|
||||
../../../src/char_str_indexer.h
|
||||
../../../src/char_str_indexer.c
|
||||
../../../src/dna_seq_indexer.h
|
||||
../../../src/dna_seq_indexer.c
|
||||
../../../src/encode.c
|
||||
../../../src/encode.h
|
||||
../../../src/uint8_indexer.c
|
||||
../../../src/uint8_indexer.h
|
||||
../../../src/build_reference_db.c
|
||||
../../../src/build_reference_db.h
|
||||
../../../src/kmer_similarity.c
|
||||
../../../src/kmer_similarity.h
|
||||
../../../src/obi_clean.c
|
||||
../../../src/obi_clean.h
|
||||
../../../src/obi_ecopcr.c
|
||||
../../../src/obi_ecopcr.h
|
||||
../../../src/obi_ecotag.c
|
||||
../../../src/obi_ecotag.h
|
||||
../../../src/obidms_taxonomy.c
|
||||
../../../src/obidms_taxonomy.h
|
||||
../../../src/obilittlebigman.c
|
||||
../../../src/obilittlebigman.h
|
||||
../../../src/_sse.h
|
||||
../../../src/obidebug.h
|
||||
../../../src/libecoPCR/libapat/CODES/dft_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/dna_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/prot_code.h
|
||||
../../../src/libecoPCR/libapat/apat_parse.c
|
||||
../../../src/libecoPCR/libapat/apat_search.c
|
||||
../../../src/libecoPCR/libapat/apat.h
|
||||
../../../src/libecoPCR/libapat/Gmach.h
|
||||
../../../src/libecoPCR/libapat/Gtypes.h
|
||||
../../../src/libecoPCR/libapat/libstki.c
|
||||
../../../src/libecoPCR/libapat/libstki.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.c
|
||||
../../../src/libecoPCR/ecoapat.c
|
||||
../../../src/libecoPCR/ecodna.c
|
||||
../../../src/libecoPCR/ecoError.c
|
||||
../../../src/libecoPCR/ecoMalloc.c
|
||||
../../../src/libecoPCR/ecoPCR.h
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
0
python/obitools3/apps/command.pxd
Executable file → Normal file
0
python/obitools3/apps/command.pxd
Executable file → Normal file
0
python/obitools3/apps/command.pyx
Executable file → Normal file
0
python/obitools3/apps/command.pyx
Executable file → Normal file
@ -1,110 +0,0 @@
|
||||
../../../src/obi_lcs.h
|
||||
../../../src/obi_lcs.c
|
||||
../../../src/obierrno.h
|
||||
../../../src/obierrno.c
|
||||
../../../src/upperband.h
|
||||
../../../src/upperband.c
|
||||
../../../src/sse_banded_LCS_alignment.h
|
||||
../../../src/sse_banded_LCS_alignment.c
|
||||
../../../src/obiblob.h
|
||||
../../../src/obiblob.c
|
||||
../../../src/utils.h
|
||||
../../../src/utils.c
|
||||
../../../src/obidms.h
|
||||
../../../src/obidms.c
|
||||
../../../src/libjson/json_utils.h
|
||||
../../../src/libjson/json_utils.c
|
||||
../../../src/libjson/cJSON.h
|
||||
../../../src/libjson/cJSON.c
|
||||
../../../src/obiavl.h
|
||||
../../../src/obiavl.c
|
||||
../../../src/bloom.h
|
||||
../../../src/bloom.c
|
||||
../../../src/crc64.h
|
||||
../../../src/crc64.c
|
||||
../../../src/murmurhash2.h
|
||||
../../../src/murmurhash2.c
|
||||
../../../src/obidmscolumn.h
|
||||
../../../src/obidmscolumn.c
|
||||
../../../src/obitypes.h
|
||||
../../../src/obitypes.c
|
||||
../../../src/obidmscolumndir.h
|
||||
../../../src/obidmscolumndir.c
|
||||
../../../src/obiblob_indexer.h
|
||||
../../../src/obiblob_indexer.c
|
||||
../../../src/obiview.h
|
||||
../../../src/obiview.c
|
||||
../../../src/hashtable.h
|
||||
../../../src/hashtable.c
|
||||
../../../src/linked_list.h
|
||||
../../../src/linked_list.c
|
||||
../../../src/obidmscolumn_array.h
|
||||
../../../src/obidmscolumn_array.c
|
||||
../../../src/obidmscolumn_blob.h
|
||||
../../../src/obidmscolumn_blob.c
|
||||
../../../src/obidmscolumn_idx.h
|
||||
../../../src/obidmscolumn_idx.c
|
||||
../../../src/obidmscolumn_bool.h
|
||||
../../../src/obidmscolumn_bool.c
|
||||
../../../src/obidmscolumn_char.h
|
||||
../../../src/obidmscolumn_char.c
|
||||
../../../src/obidmscolumn_float.h
|
||||
../../../src/obidmscolumn_float.c
|
||||
../../../src/obidmscolumn_int.h
|
||||
../../../src/obidmscolumn_int.c
|
||||
../../../src/obidmscolumn_qual.h
|
||||
../../../src/obidmscolumn_qual.c
|
||||
../../../src/obidmscolumn_seq.h
|
||||
../../../src/obidmscolumn_seq.c
|
||||
../../../src/obidmscolumn_str.h
|
||||
../../../src/obidmscolumn_str.c
|
||||
../../../src/array_indexer.h
|
||||
../../../src/array_indexer.c
|
||||
../../../src/char_str_indexer.h
|
||||
../../../src/char_str_indexer.c
|
||||
../../../src/dna_seq_indexer.h
|
||||
../../../src/dna_seq_indexer.c
|
||||
../../../src/encode.c
|
||||
../../../src/encode.h
|
||||
../../../src/uint8_indexer.c
|
||||
../../../src/uint8_indexer.h
|
||||
../../../src/build_reference_db.c
|
||||
../../../src/build_reference_db.h
|
||||
../../../src/kmer_similarity.c
|
||||
../../../src/kmer_similarity.h
|
||||
../../../src/obi_clean.c
|
||||
../../../src/obi_clean.h
|
||||
../../../src/obi_ecopcr.c
|
||||
../../../src/obi_ecopcr.h
|
||||
../../../src/obi_ecotag.c
|
||||
../../../src/obi_ecotag.h
|
||||
../../../src/obidms_taxonomy.c
|
||||
../../../src/obidms_taxonomy.h
|
||||
../../../src/obilittlebigman.c
|
||||
../../../src/obilittlebigman.h
|
||||
../../../src/_sse.h
|
||||
../../../src/obidebug.h
|
||||
../../../src/libecoPCR/libapat/CODES/dft_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/dna_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/prot_code.h
|
||||
../../../src/libecoPCR/libapat/apat_parse.c
|
||||
../../../src/libecoPCR/libapat/apat_search.c
|
||||
../../../src/libecoPCR/libapat/apat.h
|
||||
../../../src/libecoPCR/libapat/Gmach.h
|
||||
../../../src/libecoPCR/libapat/Gtypes.h
|
||||
../../../src/libecoPCR/libapat/libstki.c
|
||||
../../../src/libecoPCR/libapat/libstki.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.c
|
||||
../../../src/libecoPCR/ecoapat.c
|
||||
../../../src/libecoPCR/ecodna.c
|
||||
../../../src/libecoPCR/ecoError.c
|
||||
../../../src/libecoPCR/ecoMalloc.c
|
||||
../../../src/libecoPCR/ecoPCR.h
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
2
python/obitools3/apps/config.pxd
Executable file → Normal file
2
python/obitools3/apps/config.pxd
Executable file → Normal file
@ -7,4 +7,4 @@ cdef dict buildDefaultConfiguration(str root_config_name,
|
||||
dict config)
|
||||
|
||||
cpdef dict getConfiguration(str root_config_name=?,
|
||||
dict config=?)
|
||||
dict config=?)
|
||||
11
python/obitools3/apps/config.pyx
Executable file → Normal file
11
python/obitools3/apps/config.pyx
Executable file → Normal file
@ -101,14 +101,3 @@ cpdef dict getConfiguration(str root_config_name="__default__",
|
||||
config['__done__']=True
|
||||
|
||||
return config
|
||||
|
||||
def logger(level, *messages):
|
||||
try:
|
||||
config=getConfiguration()
|
||||
root = config["__root_config__"]
|
||||
l = config[root]['logger']
|
||||
if config[root]['verbose']:
|
||||
getattr(l, level)(*messages)
|
||||
except:
|
||||
print(*messages,file=sys.stderr)
|
||||
|
||||
|
||||
@ -1,110 +0,0 @@
|
||||
../../../src/obi_lcs.h
|
||||
../../../src/obi_lcs.c
|
||||
../../../src/obierrno.h
|
||||
../../../src/obierrno.c
|
||||
../../../src/upperband.h
|
||||
../../../src/upperband.c
|
||||
../../../src/sse_banded_LCS_alignment.h
|
||||
../../../src/sse_banded_LCS_alignment.c
|
||||
../../../src/obiblob.h
|
||||
../../../src/obiblob.c
|
||||
../../../src/utils.h
|
||||
../../../src/utils.c
|
||||
../../../src/obidms.h
|
||||
../../../src/obidms.c
|
||||
../../../src/libjson/json_utils.h
|
||||
../../../src/libjson/json_utils.c
|
||||
../../../src/libjson/cJSON.h
|
||||
../../../src/libjson/cJSON.c
|
||||
../../../src/obiavl.h
|
||||
../../../src/obiavl.c
|
||||
../../../src/bloom.h
|
||||
../../../src/bloom.c
|
||||
../../../src/crc64.h
|
||||
../../../src/crc64.c
|
||||
../../../src/murmurhash2.h
|
||||
../../../src/murmurhash2.c
|
||||
../../../src/obidmscolumn.h
|
||||
../../../src/obidmscolumn.c
|
||||
../../../src/obitypes.h
|
||||
../../../src/obitypes.c
|
||||
../../../src/obidmscolumndir.h
|
||||
../../../src/obidmscolumndir.c
|
||||
../../../src/obiblob_indexer.h
|
||||
../../../src/obiblob_indexer.c
|
||||
../../../src/obiview.h
|
||||
../../../src/obiview.c
|
||||
../../../src/hashtable.h
|
||||
../../../src/hashtable.c
|
||||
../../../src/linked_list.h
|
||||
../../../src/linked_list.c
|
||||
../../../src/obidmscolumn_array.h
|
||||
../../../src/obidmscolumn_array.c
|
||||
../../../src/obidmscolumn_blob.h
|
||||
../../../src/obidmscolumn_blob.c
|
||||
../../../src/obidmscolumn_idx.h
|
||||
../../../src/obidmscolumn_idx.c
|
||||
../../../src/obidmscolumn_bool.h
|
||||
../../../src/obidmscolumn_bool.c
|
||||
../../../src/obidmscolumn_char.h
|
||||
../../../src/obidmscolumn_char.c
|
||||
../../../src/obidmscolumn_float.h
|
||||
../../../src/obidmscolumn_float.c
|
||||
../../../src/obidmscolumn_int.h
|
||||
../../../src/obidmscolumn_int.c
|
||||
../../../src/obidmscolumn_qual.h
|
||||
../../../src/obidmscolumn_qual.c
|
||||
../../../src/obidmscolumn_seq.h
|
||||
../../../src/obidmscolumn_seq.c
|
||||
../../../src/obidmscolumn_str.h
|
||||
../../../src/obidmscolumn_str.c
|
||||
../../../src/array_indexer.h
|
||||
../../../src/array_indexer.c
|
||||
../../../src/char_str_indexer.h
|
||||
../../../src/char_str_indexer.c
|
||||
../../../src/dna_seq_indexer.h
|
||||
../../../src/dna_seq_indexer.c
|
||||
../../../src/encode.c
|
||||
../../../src/encode.h
|
||||
../../../src/uint8_indexer.c
|
||||
../../../src/uint8_indexer.h
|
||||
../../../src/build_reference_db.c
|
||||
../../../src/build_reference_db.h
|
||||
../../../src/kmer_similarity.c
|
||||
../../../src/kmer_similarity.h
|
||||
../../../src/obi_clean.c
|
||||
../../../src/obi_clean.h
|
||||
../../../src/obi_ecopcr.c
|
||||
../../../src/obi_ecopcr.h
|
||||
../../../src/obi_ecotag.c
|
||||
../../../src/obi_ecotag.h
|
||||
../../../src/obidms_taxonomy.c
|
||||
../../../src/obidms_taxonomy.h
|
||||
../../../src/obilittlebigman.c
|
||||
../../../src/obilittlebigman.h
|
||||
../../../src/_sse.h
|
||||
../../../src/obidebug.h
|
||||
../../../src/libecoPCR/libapat/CODES/dft_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/dna_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/prot_code.h
|
||||
../../../src/libecoPCR/libapat/apat_parse.c
|
||||
../../../src/libecoPCR/libapat/apat_search.c
|
||||
../../../src/libecoPCR/libapat/apat.h
|
||||
../../../src/libecoPCR/libapat/Gmach.h
|
||||
../../../src/libecoPCR/libapat/Gtypes.h
|
||||
../../../src/libecoPCR/libapat/libstki.c
|
||||
../../../src/libecoPCR/libapat/libstki.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.c
|
||||
../../../src/libecoPCR/ecoapat.c
|
||||
../../../src/libecoPCR/ecodna.c
|
||||
../../../src/libecoPCR/ecoError.c
|
||||
../../../src/libecoPCR/ecoMalloc.c
|
||||
../../../src/libecoPCR/ecoPCR.h
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
0
python/obitools3/apps/logging.pxd
Executable file → Normal file
0
python/obitools3/apps/logging.pxd
Executable file → Normal file
6
python/obitools3/apps/logging.pyx
Executable file → Normal file
6
python/obitools3/apps/logging.pyx
Executable file → Normal file
@ -22,7 +22,7 @@ cpdef getLogger(dict config):
|
||||
logfile= config[root]['log']
|
||||
|
||||
rootlogger = logging.getLogger()
|
||||
logFormatter = logging.Formatter("%%(asctime)s [%s : %%(levelname)-5.5s] %%(message)s" % config[root]['modulename'])
|
||||
logFormatter = logging.Formatter("%(asctime)s [%(levelname)-5.5s] %(message)s")
|
||||
|
||||
stderrHandler = logging.StreamHandler(sys.stderr)
|
||||
stderrHandler.setFormatter(logFormatter)
|
||||
@ -42,7 +42,5 @@ cpdef getLogger(dict config):
|
||||
rootlogger.setLevel(loglevel)
|
||||
|
||||
config[root]['logger']=rootlogger
|
||||
config[root]['verbose']=True
|
||||
|
||||
|
||||
return rootlogger
|
||||
|
||||
|
||||
@ -1,272 +0,0 @@
|
||||
def __addInputOption(optionManager):
|
||||
|
||||
optionManager.add_argument(
|
||||
dest='obi:inputURI',
|
||||
metavar='INPUT',
|
||||
help='Data source URI')
|
||||
|
||||
|
||||
group = optionManager.add_argument_group("Restriction to a sub-part options",
|
||||
"Allows to limit analysis to a sub-part of the input")
|
||||
|
||||
group.add_argument('--skip',
|
||||
action="store", dest="obi:skip",
|
||||
metavar='<N>',
|
||||
default=None,
|
||||
type=int,
|
||||
help="skip the N first sequences")
|
||||
|
||||
group.add_argument('--only',
|
||||
action="store", dest="obi:only",
|
||||
metavar='<N>',
|
||||
default=None,
|
||||
type=int,
|
||||
help="treat only N sequences")
|
||||
|
||||
|
||||
def __addImportInputOption(optionManager):
|
||||
group = optionManager.add_argument_group("Input format options for imported files")
|
||||
|
||||
group.add_argument('--fasta-input',
|
||||
action="store_const", dest="obi:inputformat",
|
||||
default=None,
|
||||
const=b'fasta',
|
||||
help="Input file is in sanger fasta format")
|
||||
|
||||
group.add_argument('--fastq-input',
|
||||
action="store_const", dest="obi:inputformat",
|
||||
default=None,
|
||||
const=b'fastq',
|
||||
help="Input file is in fastq format")
|
||||
|
||||
group.add_argument('--embl-input',
|
||||
action="store_const", dest="obi:inputformat",
|
||||
default=None,
|
||||
const=b'embl',
|
||||
help="Input file is in embl nucleic format")
|
||||
|
||||
group.add_argument('--genbank-input',
|
||||
action="store_const", dest="obi:inputformat",
|
||||
default=None,
|
||||
const=b'genbank',
|
||||
help="Input file is in genbank nucleic format")
|
||||
|
||||
group.add_argument('--ngsfilter-input',
|
||||
action="store_const", dest="obi:inputformat",
|
||||
default=None,
|
||||
const=b'ngsfilter',
|
||||
help="Input file is an ngsfilter file")
|
||||
|
||||
group.add_argument('--ecopcr-result-input',
|
||||
action="store_const", dest="obi:inputformat",
|
||||
default=None,
|
||||
const=b'ecopcr',
|
||||
help="Input file is the result of an ecoPCR (version 2)")
|
||||
|
||||
group.add_argument('--ecoprimers-result-input',
|
||||
action="store_const", dest="obi:inputformat",
|
||||
default=None,
|
||||
const=b'ecoprimers',
|
||||
help="Input file is the result of an ecoprimers")
|
||||
|
||||
group.add_argument('--tabular-input',
|
||||
action="store_const", dest="obi:inputformat",
|
||||
default=None,
|
||||
const=b'tabular',
|
||||
help="Input file is a tabular file")
|
||||
|
||||
group.add_argument('--no-skip-on-error',
|
||||
action="store_false", dest="obi:skiperror",
|
||||
default=True,
|
||||
help="Don't skip sequence entries with parsing errors (default: they are skipped)")
|
||||
|
||||
group.add_argument('--no-quality',
|
||||
action="store_true", dest="obi:noquality",
|
||||
default=False,
|
||||
help="Do not import fastQ quality")
|
||||
|
||||
group.add_argument('--quality-sanger',
|
||||
action="store_const", dest="obi:qualityformat",
|
||||
default=None,
|
||||
const=b'sanger',
|
||||
help="Fastq quality is encoded following sanger format (standard fastq)")
|
||||
|
||||
group.add_argument('--quality-solexa',
|
||||
action="store_const", dest="obi:qualityformat",
|
||||
default=None,
|
||||
const=b'solexa',
|
||||
help="Fastq quality is encoded following solexa sequencer format")
|
||||
|
||||
group.add_argument('--nuc',
|
||||
action="store_const", dest="obi:moltype",
|
||||
default=None,
|
||||
const=b'nuc',
|
||||
help="Input file contains nucleic sequences")
|
||||
|
||||
group.add_argument('--prot',
|
||||
action="store_const", dest="obi:moltype",
|
||||
default=None,
|
||||
const=b'pep',
|
||||
help="Input file contains protein sequences")
|
||||
|
||||
group.add_argument('--input-na-string',
|
||||
action="store", dest="obi:inputnastring",
|
||||
default="NA",
|
||||
type=str,
|
||||
help="String associated with Non Available (NA) values in the input")
|
||||
|
||||
|
||||
def __addTabularInputOption(optionManager):
|
||||
group = optionManager.add_argument_group("Input format options for tabular files")
|
||||
|
||||
group.add_argument('--header',
|
||||
action="store_true", dest="obi:header",
|
||||
default=False,
|
||||
help="First line of tabular file contains column names")
|
||||
|
||||
group.add_argument('--sep',
|
||||
action="store", dest="obi:sep",
|
||||
default=None,
|
||||
type=str,
|
||||
help="Column separator")
|
||||
|
||||
group.add_argument('--dec',
|
||||
action="store", dest="obi:dec",
|
||||
default=".",
|
||||
type=str,
|
||||
help="Decimal separator")
|
||||
|
||||
group.add_argument('--strip-white',
|
||||
action="store_false", dest="obi:stripwhite",
|
||||
default=True,
|
||||
help="Remove white chars at the beginning and the end of values")
|
||||
|
||||
group.add_argument('--blank-line-skip',
|
||||
action="store_false", dest="obi:blanklineskip",
|
||||
default=True,
|
||||
help="Skip empty lines")
|
||||
|
||||
group.add_argument('--comment-char',
|
||||
action="store", dest="obi:commentchar",
|
||||
default="#",
|
||||
type=str,
|
||||
help="Lines starting by this char are considered as comment")
|
||||
|
||||
|
||||
def __addTaxdumpInputOption(optionManager): # TODO maybe not the best way to do it
|
||||
group = optionManager.add_argument_group("Input format options for taxdump")
|
||||
|
||||
group.add_argument('--taxdump',
|
||||
action="store_true", dest="obi:taxdump",
|
||||
default=False,
|
||||
help="Whether the input is a taxdump")
|
||||
|
||||
|
||||
def __addTaxonomyOption(optionManager):
|
||||
group = optionManager.add_argument_group("Input format options for taxonomy")
|
||||
|
||||
group.add_argument('--taxonomy',
|
||||
action="store", dest="obi:taxoURI",
|
||||
default=None,
|
||||
help="Taxonomy URI")
|
||||
|
||||
#TODO option bool to download taxo if URI doesn't exist
|
||||
|
||||
|
||||
def addMinimalInputOption(optionManager):
|
||||
__addInputOption(optionManager)
|
||||
|
||||
|
||||
def addImportInputOption(optionManager):
|
||||
__addInputOption(optionManager)
|
||||
__addImportInputOption(optionManager)
|
||||
|
||||
|
||||
def addTabularInputOption(optionManager):
|
||||
__addTabularInputOption(optionManager)
|
||||
|
||||
|
||||
def addTaxonomyOption(optionManager):
|
||||
__addTaxonomyOption(optionManager)
|
||||
|
||||
|
||||
def addTaxdumpInputOption(optionManager):
|
||||
__addTaxdumpInputOption(optionManager)
|
||||
|
||||
|
||||
def addAllInputOption(optionManager):
|
||||
__addInputOption(optionManager)
|
||||
__addImportInputOption(optionManager)
|
||||
__addTabularInputOption(optionManager)
|
||||
__addTaxonomyOption(optionManager)
|
||||
__addTaxdumpInputOption(optionManager)
|
||||
|
||||
|
||||
def __addOutputOption(optionManager):
|
||||
|
||||
optionManager.add_argument(
|
||||
dest='obi:outputURI',
|
||||
metavar='OUTPUT',
|
||||
help='Data destination URI')
|
||||
|
||||
|
||||
def __addDMSOutputOption(optionManager):
|
||||
group = optionManager.add_argument_group("Output options for DMS data")
|
||||
|
||||
group.add_argument('--no-create-dms',
|
||||
action="store_true", dest="obi:nocreatedms",
|
||||
default=False,
|
||||
help="Don't create an output DMS is it is not existing")
|
||||
|
||||
group.add_argument('--max-elts',
|
||||
action="store", dest="obi:maxelts",
|
||||
metavar='<N>',
|
||||
default=1000,
|
||||
type=int,
|
||||
help="Maximum number of elements per line in a column "
|
||||
"(e.g. the number of different keys in a dictionary-type "
|
||||
"key from sequence headers). If the number of different keys "
|
||||
"is greater than N, the values are stored as character strings")
|
||||
|
||||
|
||||
def __addExportOutputOption(optionManager):
|
||||
group = optionManager.add_argument_group("Output format options for exported files")
|
||||
|
||||
group.add_argument('--fasta-output',
|
||||
action="store_const", dest="obi:outputformat",
|
||||
default=None,
|
||||
const=b'fasta',
|
||||
help="Output file is in sanger fasta format")
|
||||
|
||||
group.add_argument('--fastq-output',
|
||||
action="store_const", dest="obi:outputformat",
|
||||
default=None,
|
||||
const=b'fastq',
|
||||
help="Output file is in fastq format")
|
||||
|
||||
group.add_argument('--print-na',
|
||||
action="store_true", dest="obi:printna",
|
||||
default=False,
|
||||
help="Print Non Available (NA) values in the output")
|
||||
|
||||
group.add_argument('--output-na-string',
|
||||
action="store", dest="obi:outputnastring",
|
||||
default="NA",
|
||||
type=str,
|
||||
help="String associated with Non Available (NA) values in the output")
|
||||
|
||||
|
||||
def addMinimalOutputOption(optionManager):
|
||||
__addOutputOption(optionManager)
|
||||
__addDMSOutputOption(optionManager)
|
||||
|
||||
def addExportOutputOption(optionManager):
|
||||
__addOutputOption(optionManager)
|
||||
__addExportOutputOption(optionManager)
|
||||
|
||||
|
||||
def addAllOutputOption(optionManager):
|
||||
__addOutputOption(optionManager)
|
||||
__addDMSOutputOption(optionManager)
|
||||
__addExportOutputOption(optionManager)
|
||||
|
||||
@ -1,110 +0,0 @@
|
||||
../../../src/obi_lcs.h
|
||||
../../../src/obi_lcs.c
|
||||
../../../src/obierrno.h
|
||||
../../../src/obierrno.c
|
||||
../../../src/upperband.h
|
||||
../../../src/upperband.c
|
||||
../../../src/sse_banded_LCS_alignment.h
|
||||
../../../src/sse_banded_LCS_alignment.c
|
||||
../../../src/obiblob.h
|
||||
../../../src/obiblob.c
|
||||
../../../src/utils.h
|
||||
../../../src/utils.c
|
||||
../../../src/obidms.h
|
||||
../../../src/obidms.c
|
||||
../../../src/libjson/json_utils.h
|
||||
../../../src/libjson/json_utils.c
|
||||
../../../src/libjson/cJSON.h
|
||||
../../../src/libjson/cJSON.c
|
||||
../../../src/obiavl.h
|
||||
../../../src/obiavl.c
|
||||
../../../src/bloom.h
|
||||
../../../src/bloom.c
|
||||
../../../src/crc64.h
|
||||
../../../src/crc64.c
|
||||
../../../src/murmurhash2.h
|
||||
../../../src/murmurhash2.c
|
||||
../../../src/obidmscolumn.h
|
||||
../../../src/obidmscolumn.c
|
||||
../../../src/obitypes.h
|
||||
../../../src/obitypes.c
|
||||
../../../src/obidmscolumndir.h
|
||||
../../../src/obidmscolumndir.c
|
||||
../../../src/obiblob_indexer.h
|
||||
../../../src/obiblob_indexer.c
|
||||
../../../src/obiview.h
|
||||
../../../src/obiview.c
|
||||
../../../src/hashtable.h
|
||||
../../../src/hashtable.c
|
||||
../../../src/linked_list.h
|
||||
../../../src/linked_list.c
|
||||
../../../src/obidmscolumn_array.h
|
||||
../../../src/obidmscolumn_array.c
|
||||
../../../src/obidmscolumn_blob.h
|
||||
../../../src/obidmscolumn_blob.c
|
||||
../../../src/obidmscolumn_idx.h
|
||||
../../../src/obidmscolumn_idx.c
|
||||
../../../src/obidmscolumn_bool.h
|
||||
../../../src/obidmscolumn_bool.c
|
||||
../../../src/obidmscolumn_char.h
|
||||
../../../src/obidmscolumn_char.c
|
||||
../../../src/obidmscolumn_float.h
|
||||
../../../src/obidmscolumn_float.c
|
||||
../../../src/obidmscolumn_int.h
|
||||
../../../src/obidmscolumn_int.c
|
||||
../../../src/obidmscolumn_qual.h
|
||||
../../../src/obidmscolumn_qual.c
|
||||
../../../src/obidmscolumn_seq.h
|
||||
../../../src/obidmscolumn_seq.c
|
||||
../../../src/obidmscolumn_str.h
|
||||
../../../src/obidmscolumn_str.c
|
||||
../../../src/array_indexer.h
|
||||
../../../src/array_indexer.c
|
||||
../../../src/char_str_indexer.h
|
||||
../../../src/char_str_indexer.c
|
||||
../../../src/dna_seq_indexer.h
|
||||
../../../src/dna_seq_indexer.c
|
||||
../../../src/encode.c
|
||||
../../../src/encode.h
|
||||
../../../src/uint8_indexer.c
|
||||
../../../src/uint8_indexer.h
|
||||
../../../src/build_reference_db.c
|
||||
../../../src/build_reference_db.h
|
||||
../../../src/kmer_similarity.c
|
||||
../../../src/kmer_similarity.h
|
||||
../../../src/obi_clean.c
|
||||
../../../src/obi_clean.h
|
||||
../../../src/obi_ecopcr.c
|
||||
../../../src/obi_ecopcr.h
|
||||
../../../src/obi_ecotag.c
|
||||
../../../src/obi_ecotag.h
|
||||
../../../src/obidms_taxonomy.c
|
||||
../../../src/obidms_taxonomy.h
|
||||
../../../src/obilittlebigman.c
|
||||
../../../src/obilittlebigman.h
|
||||
../../../src/_sse.h
|
||||
../../../src/obidebug.h
|
||||
../../../src/libecoPCR/libapat/CODES/dft_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/dna_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/prot_code.h
|
||||
../../../src/libecoPCR/libapat/apat_parse.c
|
||||
../../../src/libecoPCR/libapat/apat_search.c
|
||||
../../../src/libecoPCR/libapat/apat.h
|
||||
../../../src/libecoPCR/libapat/Gmach.h
|
||||
../../../src/libecoPCR/libapat/Gtypes.h
|
||||
../../../src/libecoPCR/libapat/libstki.c
|
||||
../../../src/libecoPCR/libapat/libstki.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.c
|
||||
../../../src/libecoPCR/ecoapat.c
|
||||
../../../src/libecoPCR/ecodna.c
|
||||
../../../src/libecoPCR/ecoError.c
|
||||
../../../src/libecoPCR/ecoMalloc.c
|
||||
../../../src/libecoPCR/ecoPCR.h
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
6
python/obitools3/apps/progress.pxd
Executable file → Normal file
6
python/obitools3/apps/progress.pxd
Executable file → Normal file
@ -1,9 +1,10 @@
|
||||
#cython: language_level=3
|
||||
|
||||
from ..utils cimport str2bytes
|
||||
|
||||
cdef extern from "stdio.h":
|
||||
struct FILE
|
||||
int fprintf(FILE *stream, char *format, ...)
|
||||
int fputs(char *string, FILE *stream)
|
||||
FILE* stderr
|
||||
ctypedef unsigned int off_t "unsigned long long"
|
||||
|
||||
@ -51,9 +52,8 @@ cdef class ProgressBar:
|
||||
cdef int lastlog
|
||||
cdef bint ontty
|
||||
cdef int fd
|
||||
cdef bint cut
|
||||
|
||||
cdef bytes _head
|
||||
cdef bytes head
|
||||
cdef char *chead
|
||||
|
||||
cdef object logger
|
||||
|
||||
75
python/obitools3/apps/progress.pyx
Executable file → Normal file
75
python/obitools3/apps/progress.pyx
Executable file → Normal file
@ -6,14 +6,10 @@ Created on 27 mars 2016
|
||||
@author: coissac
|
||||
'''
|
||||
|
||||
|
||||
from ..utils cimport str2bytes, bytes2str
|
||||
from .config cimport getConfiguration
|
||||
import sys
|
||||
|
||||
from ..utils cimport bytes2str
|
||||
|
||||
cdef class ProgressBar:
|
||||
|
||||
cdef clock_t clock(self):
|
||||
cdef clock_t t
|
||||
cdef timeval tp
|
||||
@ -25,14 +21,11 @@ cdef class ProgressBar:
|
||||
|
||||
return t
|
||||
|
||||
|
||||
def __init__(self,
|
||||
off_t maxi,
|
||||
dict config={},
|
||||
dict config,
|
||||
str head="",
|
||||
double seconde=0.1,
|
||||
cut=False):
|
||||
|
||||
double seconde=0.1):
|
||||
self.starttime = self.clock()
|
||||
self.lasttime = self.starttime
|
||||
self.tickcount = <clock_t> (seconde * CLOCKS_PER_SEC)
|
||||
@ -41,18 +34,15 @@ cdef class ProgressBar:
|
||||
self.arrow = 0
|
||||
self.lastlog = 0
|
||||
|
||||
if not config:
|
||||
config=getConfiguration()
|
||||
|
||||
self.ontty = sys.stderr.isatty()
|
||||
|
||||
if (maxi<=0):
|
||||
maxi=1
|
||||
|
||||
self.maxi = maxi
|
||||
self.head = head
|
||||
self.chead = self._head
|
||||
self.cut = cut
|
||||
self.maxi = maxi
|
||||
self.head = str2bytes(head)
|
||||
self.chead= self.head
|
||||
|
||||
|
||||
self.logger=config[config["__root_config__"]]["logger"]
|
||||
self.wheel = '|/-\\'
|
||||
@ -66,9 +56,8 @@ cdef class ProgressBar:
|
||||
'##########' \
|
||||
'##########' \
|
||||
'##########'
|
||||
|
||||
|
||||
def __call__(self, object pos, bint force=False):
|
||||
|
||||
def __call__(self,object pos):
|
||||
cdef off_t ipos
|
||||
cdef clock_t elapsed
|
||||
cdef clock_t newtime
|
||||
@ -82,7 +71,7 @@ cdef class ProgressBar:
|
||||
|
||||
self.cycle+=1
|
||||
|
||||
if self.cycle % self.freq == 0 or force:
|
||||
if self.cycle % self.freq == 0:
|
||||
self.cycle=1
|
||||
newtime = self.clock()
|
||||
delta = newtime - self.lasttime
|
||||
@ -115,43 +104,35 @@ cdef class ProgressBar:
|
||||
if self.ontty:
|
||||
fraction=<int>(percent * 50.)
|
||||
self.arrow=(self.arrow+1) % 4
|
||||
self.diese[fraction]=0
|
||||
self.spaces[50 - fraction]=0
|
||||
|
||||
if days:
|
||||
<void>fprintf(stderr,b'\r%s %5.1f %% |%.*s%c%.*s] remain : %d days %02d:%02d:%02d\033[K',
|
||||
<void>fprintf(stderr,b'\r%s %5.1f %% |%s%c%s] remain : %d days %02d:%02d:%02d',
|
||||
self.chead,
|
||||
percent*100,
|
||||
fraction,self.diese,
|
||||
self.wheel[self.arrow],
|
||||
50-fraction,self.spaces,
|
||||
self.diese,self.wheel[self.arrow],self.spaces,
|
||||
days,hour,minu,sec)
|
||||
else:
|
||||
<void>fprintf(stderr,b'\r%s %5.1f %% |%.*s%c%.*s] remain : %02d:%02d:%02d\033[K',
|
||||
<void>fprintf(stderr,b'\r%s %5.1f %% |%s%c%s] remain : %02d:%02d:%02d',
|
||||
self.chead,
|
||||
percent*100.,
|
||||
fraction,self.diese,
|
||||
self.wheel[self.arrow],
|
||||
50-fraction,self.spaces,
|
||||
self.diese,self.wheel[self.arrow],self.spaces,
|
||||
hour,minu,sec)
|
||||
self.diese[fraction]=b'#'
|
||||
self.spaces[50 - fraction]=b' '
|
||||
|
||||
if self.cut:
|
||||
tenth = int(percent * 10)
|
||||
if tenth != self.lastlog:
|
||||
twentyth = int(percent * 20)
|
||||
if twentyth != self.lastlog:
|
||||
|
||||
if self.ontty:
|
||||
<void>fprintf(stderr,b'\n')
|
||||
|
||||
if self.ontty:
|
||||
<void>fputs(b'\n',stderr)
|
||||
|
||||
self.logger.info('%s %5.1f %% remain : %02d:%02d:%02d\033[K' % (
|
||||
bytes2str(self._head),
|
||||
percent*100.,
|
||||
hour,minu,sec))
|
||||
self.lastlog=tenth
|
||||
self.logger.info('%s %5.1f %% remain : %02d:%02d:%02d' % (
|
||||
bytes2str(self.head),
|
||||
percent*100.,
|
||||
hour,minu,sec))
|
||||
self.lastlog=twentyth
|
||||
else:
|
||||
self.cycle+=1
|
||||
|
||||
|
||||
property head:
|
||||
def __get__(self):
|
||||
return self._head
|
||||
def __set__(self,str value):
|
||||
self._head=str2bytes(value)
|
||||
self.chead=self._head
|
||||
|
||||
@ -1,110 +0,0 @@
|
||||
../../../src/obi_lcs.h
|
||||
../../../src/obi_lcs.c
|
||||
../../../src/obierrno.h
|
||||
../../../src/obierrno.c
|
||||
../../../src/upperband.h
|
||||
../../../src/upperband.c
|
||||
../../../src/sse_banded_LCS_alignment.h
|
||||
../../../src/sse_banded_LCS_alignment.c
|
||||
../../../src/obiblob.h
|
||||
../../../src/obiblob.c
|
||||
../../../src/utils.h
|
||||
../../../src/utils.c
|
||||
../../../src/obidms.h
|
||||
../../../src/obidms.c
|
||||
../../../src/libjson/json_utils.h
|
||||
../../../src/libjson/json_utils.c
|
||||
../../../src/libjson/cJSON.h
|
||||
../../../src/libjson/cJSON.c
|
||||
../../../src/obiavl.h
|
||||
../../../src/obiavl.c
|
||||
../../../src/bloom.h
|
||||
../../../src/bloom.c
|
||||
../../../src/crc64.h
|
||||
../../../src/crc64.c
|
||||
../../../src/murmurhash2.h
|
||||
../../../src/murmurhash2.c
|
||||
../../../src/obidmscolumn.h
|
||||
../../../src/obidmscolumn.c
|
||||
../../../src/obitypes.h
|
||||
../../../src/obitypes.c
|
||||
../../../src/obidmscolumndir.h
|
||||
../../../src/obidmscolumndir.c
|
||||
../../../src/obiblob_indexer.h
|
||||
../../../src/obiblob_indexer.c
|
||||
../../../src/obiview.h
|
||||
../../../src/obiview.c
|
||||
../../../src/hashtable.h
|
||||
../../../src/hashtable.c
|
||||
../../../src/linked_list.h
|
||||
../../../src/linked_list.c
|
||||
../../../src/obidmscolumn_array.h
|
||||
../../../src/obidmscolumn_array.c
|
||||
../../../src/obidmscolumn_blob.h
|
||||
../../../src/obidmscolumn_blob.c
|
||||
../../../src/obidmscolumn_idx.h
|
||||
../../../src/obidmscolumn_idx.c
|
||||
../../../src/obidmscolumn_bool.h
|
||||
../../../src/obidmscolumn_bool.c
|
||||
../../../src/obidmscolumn_char.h
|
||||
../../../src/obidmscolumn_char.c
|
||||
../../../src/obidmscolumn_float.h
|
||||
../../../src/obidmscolumn_float.c
|
||||
../../../src/obidmscolumn_int.h
|
||||
../../../src/obidmscolumn_int.c
|
||||
../../../src/obidmscolumn_qual.h
|
||||
../../../src/obidmscolumn_qual.c
|
||||
../../../src/obidmscolumn_seq.h
|
||||
../../../src/obidmscolumn_seq.c
|
||||
../../../src/obidmscolumn_str.h
|
||||
../../../src/obidmscolumn_str.c
|
||||
../../../src/array_indexer.h
|
||||
../../../src/array_indexer.c
|
||||
../../../src/char_str_indexer.h
|
||||
../../../src/char_str_indexer.c
|
||||
../../../src/dna_seq_indexer.h
|
||||
../../../src/dna_seq_indexer.c
|
||||
../../../src/encode.c
|
||||
../../../src/encode.h
|
||||
../../../src/uint8_indexer.c
|
||||
../../../src/uint8_indexer.h
|
||||
../../../src/build_reference_db.c
|
||||
../../../src/build_reference_db.h
|
||||
../../../src/kmer_similarity.c
|
||||
../../../src/kmer_similarity.h
|
||||
../../../src/obi_clean.c
|
||||
../../../src/obi_clean.h
|
||||
../../../src/obi_ecopcr.c
|
||||
../../../src/obi_ecopcr.h
|
||||
../../../src/obi_ecotag.c
|
||||
../../../src/obi_ecotag.h
|
||||
../../../src/obidms_taxonomy.c
|
||||
../../../src/obidms_taxonomy.h
|
||||
../../../src/obilittlebigman.c
|
||||
../../../src/obilittlebigman.h
|
||||
../../../src/_sse.h
|
||||
../../../src/obidebug.h
|
||||
../../../src/libecoPCR/libapat/CODES/dft_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/dna_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/prot_code.h
|
||||
../../../src/libecoPCR/libapat/apat_parse.c
|
||||
../../../src/libecoPCR/libapat/apat_search.c
|
||||
../../../src/libecoPCR/libapat/apat.h
|
||||
../../../src/libecoPCR/libapat/Gmach.h
|
||||
../../../src/libecoPCR/libapat/Gtypes.h
|
||||
../../../src/libecoPCR/libapat/libstki.c
|
||||
../../../src/libecoPCR/libapat/libstki.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.c
|
||||
../../../src/libecoPCR/ecoapat.c
|
||||
../../../src/libecoPCR/ecodna.c
|
||||
../../../src/libecoPCR/ecoError.c
|
||||
../../../src/libecoPCR/ecoMalloc.c
|
||||
../../../src/libecoPCR/ecoPCR.h
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
@ -1,10 +0,0 @@
|
||||
#cython: language_level=3
|
||||
|
||||
'''
|
||||
Created on 28 juillet 2017
|
||||
|
||||
@author: coissac
|
||||
'''
|
||||
|
||||
from obitools3.dms.dms cimport DMS
|
||||
from obitools3.utils cimport tobytes,tostr
|
||||
@ -1,96 +0,0 @@
|
||||
#cython: language_level=3
|
||||
|
||||
'''
|
||||
Created on 28 juillet 2017
|
||||
|
||||
@author: coissac
|
||||
'''
|
||||
|
||||
from os import environb,getpid
|
||||
from os.path import join, isdir
|
||||
from tempfile import TemporaryDirectory, _get_candidate_names
|
||||
from shutil import rmtree
|
||||
from atexit import register
|
||||
|
||||
from obitools3.dms.dms import DMS
|
||||
|
||||
from obitools3.apps.config import getConfiguration
|
||||
from obitools3.apps.config import logger
|
||||
|
||||
cpdef get_temp_dir():
|
||||
"""
|
||||
Returns a temporary directory object specific of this instance of obitools.
|
||||
|
||||
This is an application function. It cannot be called out of an obi command.
|
||||
It requires a valid configuration.
|
||||
|
||||
If the function is called several time from the same obi session, the same
|
||||
directory is returned.
|
||||
|
||||
If the OBITMP environment variable exist, the temporary directory is created
|
||||
inside this directory.
|
||||
|
||||
The directory is automatically destroyed at the end of the end of the process.
|
||||
|
||||
@return: a temporary python directory object.
|
||||
"""
|
||||
cdef bytes tmpdirname
|
||||
cdef dict config = getConfiguration()
|
||||
|
||||
root = config["__root_config__"]
|
||||
|
||||
try:
|
||||
return config[root]["tempdir"].name
|
||||
except KeyError:
|
||||
pass
|
||||
|
||||
try:
|
||||
basedir=environb[b'OBITMP']
|
||||
except KeyError:
|
||||
basedir=None
|
||||
|
||||
tmp = TemporaryDirectory(dir=basedir)
|
||||
|
||||
config[root]["tempdir"]=tmp
|
||||
|
||||
return tmp.name
|
||||
|
||||
cpdef get_temp_dir_name():
|
||||
"""
|
||||
Returns the name of the temporary directory object
|
||||
specific of this instance of obitools.
|
||||
|
||||
@return: the name of the temporary directory.
|
||||
|
||||
@see get_temp_dir
|
||||
"""
|
||||
return get_temp_dir_name().name
|
||||
|
||||
|
||||
cpdef get_temp_dms():
|
||||
|
||||
cdef bytes tmpdirname # @DuplicatedSignature
|
||||
cdef dict config = getConfiguration() # @DuplicatedSignature
|
||||
cdef DMS tmpdms
|
||||
|
||||
root = config["__root_config__"]
|
||||
|
||||
try:
|
||||
return config[root]["tempdms"]
|
||||
except KeyError:
|
||||
pass
|
||||
|
||||
tmpdirname=get_temp_dir()
|
||||
|
||||
tempname = join(tmpdirname,
|
||||
b"obi.%d.%s" % (getpid(),
|
||||
tobytes(next(_get_candidate_names())))
|
||||
)
|
||||
|
||||
tmpdms = DMS.new(tempname)
|
||||
|
||||
config[root]["tempdms"]=tmpdms
|
||||
|
||||
return tmpdms
|
||||
|
||||
|
||||
0
python/obitools3/commands/__init__.py
Executable file → Normal file
0
python/obitools3/commands/__init__.py
Executable file → Normal file
@ -1,103 +0,0 @@
|
||||
../../../src/obi_lcs.h
|
||||
../../../src/obi_lcs.c
|
||||
../../../src/obierrno.h
|
||||
../../../src/obierrno.c
|
||||
../../../src/upperband.h
|
||||
../../../src/upperband.c
|
||||
../../../src/sse_banded_LCS_alignment.h
|
||||
../../../src/sse_banded_LCS_alignment.c
|
||||
../../../src/obiblob.h
|
||||
../../../src/obiblob.c
|
||||
../../../src/utils.h
|
||||
../../../src/utils.c
|
||||
../../../src/obidms.h
|
||||
../../../src/obidms.c
|
||||
../../../src/libjson/json_utils.h
|
||||
../../../src/libjson/json_utils.c
|
||||
../../../src/libjson/cJSON.h
|
||||
../../../src/libjson/cJSON.c
|
||||
../../../src/obiavl.h
|
||||
../../../src/obiavl.c
|
||||
../../../src/bloom.h
|
||||
../../../src/bloom.c
|
||||
../../../src/crc64.h
|
||||
../../../src/crc64.c
|
||||
../../../src/murmurhash2.h
|
||||
../../../src/murmurhash2.c
|
||||
../../../src/obidmscolumn.h
|
||||
../../../src/obidmscolumn.c
|
||||
../../../src/obitypes.h
|
||||
../../../src/obitypes.c
|
||||
../../../src/obidmscolumndir.h
|
||||
../../../src/obidmscolumndir.c
|
||||
../../../src/obiblob_indexer.h
|
||||
../../../src/obiblob_indexer.c
|
||||
../../../src/obiview.h
|
||||
../../../src/obiview.c
|
||||
../../../src/hashtable.h
|
||||
../../../src/hashtable.c
|
||||
../../../src/linked_list.h
|
||||
../../../src/linked_list.c
|
||||
../../../src/obidmscolumn_array.h
|
||||
../../../src/obidmscolumn_array.c
|
||||
../../../src/obidmscolumn_blob.h
|
||||
../../../src/obidmscolumn_blob.c
|
||||
../../../src/obidmscolumn_idx.h
|
||||
../../../src/obidmscolumn_idx.c
|
||||
../../../src/obidmscolumn_bool.h
|
||||
../../../src/obidmscolumn_bool.c
|
||||
../../../src/obidmscolumn_char.h
|
||||
../../../src/obidmscolumn_char.c
|
||||
../../../src/obidmscolumn_float.h
|
||||
../../../src/obidmscolumn_float.c
|
||||
../../../src/obidmscolumn_int.h
|
||||
../../../src/obidmscolumn_int.c
|
||||
../../../src/obidmscolumn_qual.h
|
||||
../../../src/obidmscolumn_qual.c
|
||||
../../../src/obidmscolumn_seq.h
|
||||
../../../src/obidmscolumn_seq.c
|
||||
../../../src/obidmscolumn_str.h
|
||||
../../../src/obidmscolumn_str.c
|
||||
../../../src/array_indexer.h
|
||||
../../../src/array_indexer.c
|
||||
../../../src/char_str_indexer.h
|
||||
../../../src/char_str_indexer.c
|
||||
../../../src/dna_seq_indexer.h
|
||||
../../../src/dna_seq_indexer.c
|
||||
../../../src/encode.c
|
||||
../../../src/encode.h
|
||||
../../../src/uint8_indexer.c
|
||||
../../../src/uint8_indexer.h
|
||||
../../../src/build_reference_db.c
|
||||
../../../src/build_reference_db.h
|
||||
../../../src/kmer_similarity.c
|
||||
../../../src/kmer_similarity.h
|
||||
../../../src/obi_clean.c
|
||||
../../../src/obi_clean.h
|
||||
../../../src/obi_ecopcr.c
|
||||
../../../src/obi_ecopcr.h
|
||||
../../../src/obi_ecotag.c
|
||||
../../../src/obi_ecotag.h
|
||||
../../../src/obidms_taxonomy.c
|
||||
../../../src/obidms_taxonomy.h
|
||||
../../../src/obilittlebigman.c
|
||||
../../../src/obilittlebigman.h
|
||||
../../../src/_sse.h
|
||||
../../../src/obidebug.h
|
||||
../../../src/libecoPCR/libapat/CODES/dft_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/dna_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/prot_code.h
|
||||
../../../src/libecoPCR/libapat/apat_parse.c
|
||||
../../../src/libecoPCR/libapat/apat_search.c
|
||||
../../../src/libecoPCR/libapat/apat.h
|
||||
../../../src/libecoPCR/libapat/Gmach.h
|
||||
../../../src/libecoPCR/libapat/Gtypes.h
|
||||
../../../src/libecoPCR/libapat/libstki.c
|
||||
../../../src/libecoPCR/libapat/libstki.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.c
|
||||
../../../src/libecoPCR/ecoapat.c
|
||||
../../../src/libecoPCR/ecodna.c
|
||||
../../../src/libecoPCR/ecoError.c
|
||||
../../../src/libecoPCR/ecoMalloc.c
|
||||
../../../src/libecoPCR/ecoPCR.h
|
||||
@ -1,18 +0,0 @@
|
||||
#cython: language_level=3
|
||||
|
||||
|
||||
cpdef align_columns(bytes dms_n,
|
||||
bytes input_view_1_n,
|
||||
bytes output_view_n,
|
||||
bytes input_view_2_n=*,
|
||||
bytes input_column_1_n=*,
|
||||
bytes input_column_2_n=*,
|
||||
bytes input_elt_1_n=*,
|
||||
bytes input_elt_2_n=*,
|
||||
bytes id_column_1_n=*,
|
||||
bytes id_column_2_n=*,
|
||||
double threshold=*, bint normalize=*,
|
||||
int reference=*, bint similarity_mode=*,
|
||||
bint print_seq=*, bint print_count=*,
|
||||
bytes comments=*,
|
||||
int thread_count=*)
|
||||
@ -1,274 +0,0 @@
|
||||
#cython: language_level=3
|
||||
|
||||
from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport
|
||||
from obitools3.dms import DMS
|
||||
from obitools3.dms.view.view cimport View
|
||||
from obitools3.uri.decode import open_uri
|
||||
from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption
|
||||
from obitools3.dms.view import RollbackException
|
||||
from obitools3.apps.config import logger
|
||||
from obitools3.utils cimport tobytes, str2bytes
|
||||
|
||||
from obitools3.dms.capi.obilcsalign cimport obi_lcs_align_one_column, \
|
||||
obi_lcs_align_two_columns
|
||||
|
||||
import time
|
||||
import sys
|
||||
|
||||
|
||||
__title__="Aligns one sequence column with itself or two sequence columns"
|
||||
|
||||
|
||||
def addOptions(parser):
|
||||
|
||||
addMinimalInputOption(parser)
|
||||
addMinimalOutputOption(parser)
|
||||
|
||||
group=parser.add_argument_group('obi align specific options')
|
||||
|
||||
group.add_argument('--input-2', '-I',
|
||||
action="store", dest="align:inputuri2",
|
||||
metavar='<INPUT URI>',
|
||||
default="",
|
||||
type=str,
|
||||
help="Eventually, the URI of the second input to align with the first one.")
|
||||
|
||||
group.add_argument('--threshold','-t',
|
||||
action="store", dest="align:threshold",
|
||||
metavar='<THRESHOLD>',
|
||||
default=0.0,
|
||||
type=float,
|
||||
help="Score threshold. If the score is normalized and expressed in similarity (default),"
|
||||
" it is an identity, e.g. 0.95 for an identity of 95%%. If the score is normalized"
|
||||
" and expressed in distance, it is (1.0 - identity), e.g. 0.05 for an identity of 95%%."
|
||||
" If the score is not normalized and expressed in similarity, it is the length of the"
|
||||
" Longest Common Subsequence. If the score is not normalized and expressed in distance,"
|
||||
" it is (reference length - LCS length)."
|
||||
" Only sequence pairs with a similarity above <THRESHOLD> are printed. Default: 0.00"
|
||||
" (no threshold).")
|
||||
|
||||
group.add_argument('--longest-length','-L',
|
||||
action="store_const", dest="align:reflength",
|
||||
default=0,
|
||||
const=1,
|
||||
help="The reference length is the length of the longest sequence."
|
||||
" Default: the reference length is the length of the alignment.")
|
||||
|
||||
group.add_argument('--shortest-length','-l',
|
||||
action="store_const", dest="align:reflength",
|
||||
default=0,
|
||||
const=2,
|
||||
help="The reference length is the length of the shortest sequence."
|
||||
" Default: the reference length is the length of the alignment.")
|
||||
|
||||
group.add_argument('--raw','-r',
|
||||
action="store_false", dest="align:normalize",
|
||||
default=True,
|
||||
help="Raw score, not normalized. Default: score is normalized with the reference sequence length.")
|
||||
|
||||
group.add_argument('--distance','-D',
|
||||
action="store_false", dest="align:similarity",
|
||||
default=True,
|
||||
help="Score is expressed in distance. Default: score is expressed in similarity.")
|
||||
|
||||
group.add_argument('--print-seq','-s',
|
||||
action="store_true", dest="align:printseq",
|
||||
default=False,
|
||||
help="The nucleotide sequences are written in the output view. Default: they are not written.")
|
||||
|
||||
group.add_argument('--print-count','-n',
|
||||
action="store_true", dest="align:printcount",
|
||||
default=False,
|
||||
help="Sequence counts are written in the output view. Default: they are not written.")
|
||||
|
||||
group.add_argument('--thread-count','-p', # TODO should probably be in a specific option group
|
||||
action="store", dest="align:threadcount",
|
||||
metavar='<THREAD COUNT>',
|
||||
default=1,
|
||||
type=int,
|
||||
help="Number of threads to use for the computation. Default: one.")
|
||||
|
||||
|
||||
cpdef align_columns(bytes dms_n,
|
||||
bytes input_view_1_n,
|
||||
bytes output_view_n,
|
||||
bytes input_view_2_n=b"",
|
||||
bytes input_column_1_n=b"",
|
||||
bytes input_column_2_n=b"",
|
||||
bytes input_elt_1_n=b"",
|
||||
bytes input_elt_2_n=b"",
|
||||
bytes id_column_1_n=b"",
|
||||
bytes id_column_2_n=b"",
|
||||
double threshold=0.0, bint normalize=True,
|
||||
int reference=0, bint similarity_mode=True,
|
||||
bint print_seq=False, bint print_count=False,
|
||||
bytes comments=b"{}",
|
||||
int thread_count=1) :
|
||||
|
||||
if input_view_2_n == b"" and input_column_2_n == b"" :
|
||||
if obi_lcs_align_one_column(dms_n, \
|
||||
input_view_1_n, \
|
||||
input_column_1_n, \
|
||||
input_elt_1_n, \
|
||||
id_column_1_n, \
|
||||
output_view_n, \
|
||||
comments, \
|
||||
print_seq, \
|
||||
print_count, \
|
||||
threshold, normalize, reference, similarity_mode,
|
||||
thread_count) < 0 :
|
||||
raise Exception("Error aligning sequences")
|
||||
|
||||
else:
|
||||
if obi_lcs_align_two_columns(dms_n, \
|
||||
input_view_1_n, \
|
||||
input_view_2_n, \
|
||||
input_column_1_n, \
|
||||
input_column_2_n, \
|
||||
input_elt_1_n, \
|
||||
input_elt_2_n, \
|
||||
id_column_1_n, \
|
||||
id_column_2_n, \
|
||||
output_view_n, \
|
||||
comments, \
|
||||
print_seq, \
|
||||
print_count, \
|
||||
threshold, normalize, reference, similarity_mode) < 0 :
|
||||
raise Exception("Error aligning sequences")
|
||||
|
||||
|
||||
def run(config):
|
||||
|
||||
DMS.obi_atexit()
|
||||
|
||||
logger("info", "obi align")
|
||||
|
||||
# Open the input: only the DMS
|
||||
input = open_uri(config['obi']['inputURI'],
|
||||
dms_only=True)
|
||||
if input is None:
|
||||
raise Exception("Could not read input")
|
||||
i_dms = input[0]
|
||||
i_dms_name = input[0].name
|
||||
i_uri = input[1]
|
||||
i_view_name = i_uri.split(b"/")[0]
|
||||
i_column_name = b""
|
||||
i_element_name = b""
|
||||
if len(i_uri.split(b"/")) == 2:
|
||||
i_column_name = i_uri.split(b"/")[1]
|
||||
if len(i_uri.split(b"/")) == 3:
|
||||
i_element_name = i_uri.split(b"/")[2]
|
||||
if len(i_uri.split(b"/")) > 3:
|
||||
raise Exception("Input URI contains too many elements:", config['obi']['inputURI'])
|
||||
|
||||
# Open the second input if there is one
|
||||
i_dms_2 = None
|
||||
i_dms_name_2 = b""
|
||||
original_i_view_name_2 = b""
|
||||
i_view_name_2 = b""
|
||||
i_column_name_2 = b""
|
||||
i_element_name_2 = b""
|
||||
if config['align']['inputuri2']:
|
||||
input_2 = open_uri(config['align']['inputuri2'],
|
||||
dms_only=True)
|
||||
if input_2 is None:
|
||||
raise Exception("Could not read second input")
|
||||
i_dms_2 = input_2[0]
|
||||
i_dms_name_2 = i_dms_2.name
|
||||
i_uri_2 = input_2[1]
|
||||
original_i_view_name_2 = i_uri_2.split(b"/")[0]
|
||||
if len(i_uri_2.split(b"/")) == 2:
|
||||
i_column_name_2 = i_uri_2.split(b"/")[1]
|
||||
if len(i_uri_2.split(b"/")) == 3:
|
||||
i_element_name_2 = i_uri_2.split(b"/")[2]
|
||||
if len(i_uri_2.split(b"/")) > 3:
|
||||
raise Exception("Input URI contains too many elements:", config['align']['inputuri2'])
|
||||
|
||||
# If the 2 input DMS are not the same, temporarily import 2nd input view in first input DMS
|
||||
if i_dms != i_dms_2:
|
||||
temp_i_view_name_2 = original_i_view_name_2
|
||||
i=0
|
||||
while temp_i_view_name_2 in i_dms: # Making sure view name is unique in input DMS
|
||||
temp_i_view_name_2 = original_i_view_name_2+b"_"+str2bytes(str(i))
|
||||
i+=1
|
||||
i_view_name_2 = temp_i_view_name_2
|
||||
View.import_view(i_dms_2.full_path[:-7], i_dms.full_path[:-7], original_i_view_name_2, i_view_name_2)
|
||||
|
||||
# Open the output: only the DMS
|
||||
output = open_uri(config['obi']['outputURI'],
|
||||
input=False,
|
||||
dms_only=True)
|
||||
if output is None:
|
||||
raise Exception("Could not create output")
|
||||
o_dms = output[0]
|
||||
o_dms_name = o_dms.name
|
||||
final_o_view_name = output[1]
|
||||
|
||||
# If the input and output DMS are not the same, align creating a temporary view in the input dms that will be exported to
|
||||
# the right DMS and deleted in the other afterwards.
|
||||
if i_dms != o_dms:
|
||||
temporary_view_name = final_o_view_name
|
||||
i=0
|
||||
while temporary_view_name in i_dms: # Making sure view name is unique in input DMS
|
||||
temporary_view_name = final_o_view_name+b"_"+str2bytes(str(i))
|
||||
i+=1
|
||||
o_view_name = temporary_view_name
|
||||
else:
|
||||
o_view_name = final_o_view_name
|
||||
|
||||
# Save command config in View comments
|
||||
command_line = " ".join(sys.argv[1:])
|
||||
|
||||
i_dms_list = [i_dms_name]
|
||||
if i_dms_name_2:
|
||||
i_dms_list.append(i_dms_name_2)
|
||||
i_view_list = [i_view_name]
|
||||
if original_i_view_name_2:
|
||||
i_view_list.append(original_i_view_name_2)
|
||||
comments = View.print_config(config, "align", command_line, input_dms_name=i_dms_list, input_view_name=i_view_list)
|
||||
|
||||
# Call cython alignment function
|
||||
# Using default ID columns of the view. TODO discuss adding option
|
||||
align_columns(i_dms_name, \
|
||||
i_view_name, \
|
||||
o_view_name, \
|
||||
input_view_2_n = i_view_name_2, \
|
||||
input_column_1_n = i_column_name, \
|
||||
input_column_2_n = i_column_name_2, \
|
||||
input_elt_1_n = i_element_name, \
|
||||
input_elt_2_n = i_element_name_2, \
|
||||
id_column_1_n = b"", \
|
||||
id_column_2_n = b"", \
|
||||
threshold = config['align']['threshold'], \
|
||||
normalize = config['align']['normalize'], \
|
||||
reference = config['align']['reflength'], \
|
||||
similarity_mode = config['align']['similarity'], \
|
||||
print_seq = config['align']['printseq'], \
|
||||
print_count = config['align']['printcount'], \
|
||||
comments = comments, \
|
||||
thread_count = config['align']['threadcount'])
|
||||
|
||||
# If the input and output DMS are not the same, export result view to output DMS
|
||||
if i_dms != o_dms:
|
||||
View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], o_view_name, final_o_view_name)
|
||||
|
||||
# Save command config in output DMS comments
|
||||
o_dms.record_command_line(command_line)
|
||||
|
||||
#print("\n\nOutput view:\n````````````", file=sys.stderr)
|
||||
#print(repr(o_dms[final_o_view_name]), file=sys.stderr)
|
||||
|
||||
# If the two input DMS are different, delete the temporary input view in the first input DMS
|
||||
if i_dms_2 and i_dms != i_dms_2:
|
||||
View.delete_view(i_dms, i_view_name_2)
|
||||
i_dms_2.close()
|
||||
|
||||
# If the input and the output DMS are different, delete the temporary result view in the input DMS
|
||||
if i_dms != o_dms:
|
||||
View.delete_view(i_dms, o_view_name)
|
||||
o_dms.close()
|
||||
|
||||
i_dms.close()
|
||||
|
||||
logger("info", "Done.")
|
||||
|
||||
@ -1,103 +0,0 @@
|
||||
../../../src/obi_lcs.h
|
||||
../../../src/obi_lcs.c
|
||||
../../../src/obierrno.h
|
||||
../../../src/obierrno.c
|
||||
../../../src/upperband.h
|
||||
../../../src/upperband.c
|
||||
../../../src/sse_banded_LCS_alignment.h
|
||||
../../../src/sse_banded_LCS_alignment.c
|
||||
../../../src/obiblob.h
|
||||
../../../src/obiblob.c
|
||||
../../../src/utils.h
|
||||
../../../src/utils.c
|
||||
../../../src/obidms.h
|
||||
../../../src/obidms.c
|
||||
../../../src/libjson/json_utils.h
|
||||
../../../src/libjson/json_utils.c
|
||||
../../../src/libjson/cJSON.h
|
||||
../../../src/libjson/cJSON.c
|
||||
../../../src/obiavl.h
|
||||
../../../src/obiavl.c
|
||||
../../../src/bloom.h
|
||||
../../../src/bloom.c
|
||||
../../../src/crc64.h
|
||||
../../../src/crc64.c
|
||||
../../../src/murmurhash2.h
|
||||
../../../src/murmurhash2.c
|
||||
../../../src/obidmscolumn.h
|
||||
../../../src/obidmscolumn.c
|
||||
../../../src/obitypes.h
|
||||
../../../src/obitypes.c
|
||||
../../../src/obidmscolumndir.h
|
||||
../../../src/obidmscolumndir.c
|
||||
../../../src/obiblob_indexer.h
|
||||
../../../src/obiblob_indexer.c
|
||||
../../../src/obiview.h
|
||||
../../../src/obiview.c
|
||||
../../../src/hashtable.h
|
||||
../../../src/hashtable.c
|
||||
../../../src/linked_list.h
|
||||
../../../src/linked_list.c
|
||||
../../../src/obidmscolumn_array.h
|
||||
../../../src/obidmscolumn_array.c
|
||||
../../../src/obidmscolumn_blob.h
|
||||
../../../src/obidmscolumn_blob.c
|
||||
../../../src/obidmscolumn_idx.h
|
||||
../../../src/obidmscolumn_idx.c
|
||||
../../../src/obidmscolumn_bool.h
|
||||
../../../src/obidmscolumn_bool.c
|
||||
../../../src/obidmscolumn_char.h
|
||||
../../../src/obidmscolumn_char.c
|
||||
../../../src/obidmscolumn_float.h
|
||||
../../../src/obidmscolumn_float.c
|
||||
../../../src/obidmscolumn_int.h
|
||||
../../../src/obidmscolumn_int.c
|
||||
../../../src/obidmscolumn_qual.h
|
||||
../../../src/obidmscolumn_qual.c
|
||||
../../../src/obidmscolumn_seq.h
|
||||
../../../src/obidmscolumn_seq.c
|
||||
../../../src/obidmscolumn_str.h
|
||||
../../../src/obidmscolumn_str.c
|
||||
../../../src/array_indexer.h
|
||||
../../../src/array_indexer.c
|
||||
../../../src/char_str_indexer.h
|
||||
../../../src/char_str_indexer.c
|
||||
../../../src/dna_seq_indexer.h
|
||||
../../../src/dna_seq_indexer.c
|
||||
../../../src/encode.c
|
||||
../../../src/encode.h
|
||||
../../../src/uint8_indexer.c
|
||||
../../../src/uint8_indexer.h
|
||||
../../../src/build_reference_db.c
|
||||
../../../src/build_reference_db.h
|
||||
../../../src/kmer_similarity.c
|
||||
../../../src/kmer_similarity.h
|
||||
../../../src/obi_clean.c
|
||||
../../../src/obi_clean.h
|
||||
../../../src/obi_ecopcr.c
|
||||
../../../src/obi_ecopcr.h
|
||||
../../../src/obi_ecotag.c
|
||||
../../../src/obi_ecotag.h
|
||||
../../../src/obidms_taxonomy.c
|
||||
../../../src/obidms_taxonomy.h
|
||||
../../../src/obilittlebigman.c
|
||||
../../../src/obilittlebigman.h
|
||||
../../../src/_sse.h
|
||||
../../../src/obidebug.h
|
||||
../../../src/libecoPCR/libapat/CODES/dft_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/dna_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/prot_code.h
|
||||
../../../src/libecoPCR/libapat/apat_parse.c
|
||||
../../../src/libecoPCR/libapat/apat_search.c
|
||||
../../../src/libecoPCR/libapat/apat.h
|
||||
../../../src/libecoPCR/libapat/Gmach.h
|
||||
../../../src/libecoPCR/libapat/Gtypes.h
|
||||
../../../src/libecoPCR/libapat/libstki.c
|
||||
../../../src/libecoPCR/libapat/libstki.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.c
|
||||
../../../src/libecoPCR/ecoapat.c
|
||||
../../../src/libecoPCR/ecodna.c
|
||||
../../../src/libecoPCR/ecoError.c
|
||||
../../../src/libecoPCR/ecoMalloc.c
|
||||
../../../src/libecoPCR/ecoPCR.h
|
||||
@ -1,4 +0,0 @@
|
||||
#cython: language_level=3
|
||||
|
||||
|
||||
cdef object buildAlignment(object direct, object reverse)
|
||||
@ -1,249 +0,0 @@
|
||||
#cython: language_level=3
|
||||
|
||||
from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport
|
||||
from obitools3.dms import DMS
|
||||
from obitools3.dms.view import RollbackException
|
||||
from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS
|
||||
from obitools3.dms.column.column cimport Column
|
||||
from obitools3.dms.capi.obiview cimport QUALITY_COLUMN
|
||||
from obitools3.dms.capi.obitypes cimport OBI_QUAL
|
||||
from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption
|
||||
from obitools3.uri.decode import open_uri
|
||||
from obitools3.apps.config import logger
|
||||
from obitools3.libalign._qsassemble import QSolexaReverseAssemble
|
||||
from obitools3.libalign._qsrassemble import QSolexaRightReverseAssemble
|
||||
from obitools3.libalign._solexapairend import buildConsensus, buildJoinedSequence
|
||||
from obitools3.dms.obiseq cimport Nuc_Seq
|
||||
from obitools3.libalign.shifted_ali cimport Kmer_similarity, Ali_shifted
|
||||
from obitools3.commands.ngsfilter import REVERSE_SEQ_COLUMN_NAME, REVERSE_QUALITY_COLUMN_NAME
|
||||
|
||||
import sys
|
||||
import os
|
||||
|
||||
|
||||
__title__="Aligns paired-ended reads"
|
||||
|
||||
|
||||
|
||||
def addOptions(parser):
|
||||
|
||||
addMinimalInputOption(parser)
|
||||
addMinimalOutputOption(parser)
|
||||
|
||||
group = parser.add_argument_group('obi alignpairedend specific options')
|
||||
|
||||
group.add_argument('-R', '--reverse-reads',
|
||||
action="store", dest="alignpairedend:reverse",
|
||||
metavar="<URI>",
|
||||
default=None,
|
||||
type=str,
|
||||
help="URI to the reverse reads if they are in a different view than the forward reads")
|
||||
|
||||
group.add_argument('--score-min',
|
||||
action="store", dest="alignpairedend:smin",
|
||||
metavar="#.###",
|
||||
default=None,
|
||||
type=float,
|
||||
help="Minimum score for keeping alignments")
|
||||
|
||||
group.add_argument('-A', '--true-ali',
|
||||
action="store_true", dest="alignpairedend:trueali",
|
||||
default=False,
|
||||
help="Performs gap free end alignment of sequences instead of using kmers to compute alignments (slower).")
|
||||
|
||||
group.add_argument('-k', '--kmer-size',
|
||||
action="store", dest="alignpairedend:kmersize",
|
||||
metavar="#",
|
||||
default=3,
|
||||
type=int,
|
||||
help="K-mer size for kmer comparisons, between 1 and 4 (not when using -A option; default: 3)")
|
||||
|
||||
|
||||
la = QSolexaReverseAssemble()
|
||||
ra = QSolexaRightReverseAssemble()
|
||||
cdef object buildAlignment(object direct, object reverse):
|
||||
|
||||
if len(direct)==0 or len(reverse)==0:
|
||||
return None
|
||||
|
||||
la.seqA = direct
|
||||
la.seqB = reverse
|
||||
|
||||
ali=la()
|
||||
ali.direction='left'
|
||||
|
||||
ra.seqA = direct
|
||||
ra.seqB = reverse
|
||||
|
||||
rali=ra()
|
||||
rali.direction='right'
|
||||
|
||||
if ali.score < rali.score:
|
||||
ali = rali
|
||||
|
||||
return ali
|
||||
|
||||
|
||||
def alignmentIterator(entries, aligner):
|
||||
|
||||
if type(entries) == list:
|
||||
two_views = True
|
||||
forward = entries[0]
|
||||
reverse = entries[1]
|
||||
entries_len = len(forward)
|
||||
else:
|
||||
two_views = False
|
||||
entries_len = len(entries)
|
||||
|
||||
for i in range(entries_len):
|
||||
if two_views:
|
||||
seqF = forward[i]
|
||||
seqR = reverse[i]
|
||||
else:
|
||||
seqF = Nuc_Seq.new_from_stored(entries[i])
|
||||
seqR = Nuc_Seq(seqF.id, seqF[REVERSE_SEQ_COLUMN_NAME], quality=seqF[REVERSE_QUALITY_COLUMN_NAME])
|
||||
seqR.index = i
|
||||
|
||||
ali = aligner(seqF, seqR)
|
||||
|
||||
if ali is None:
|
||||
continue
|
||||
|
||||
yield ali
|
||||
|
||||
|
||||
def run(config):
|
||||
|
||||
DMS.obi_atexit()
|
||||
|
||||
logger("info", "obi alignpairedend")
|
||||
|
||||
# Open the input
|
||||
|
||||
two_views = False
|
||||
forward = None
|
||||
reverse = None
|
||||
input = None
|
||||
|
||||
input = open_uri(config['obi']['inputURI'])
|
||||
if input is None:
|
||||
raise Exception("Could not open input reads")
|
||||
if input[2] != View_NUC_SEQS:
|
||||
raise NotImplementedError('obi alignpairedend only works on NUC_SEQS views')
|
||||
|
||||
if "reverse" in config["alignpairedend"]:
|
||||
|
||||
two_views = True
|
||||
|
||||
forward = input[1]
|
||||
|
||||
rinput = open_uri(config["alignpairedend"]["reverse"])
|
||||
if rinput is None:
|
||||
raise Exception("Could not open reverse reads")
|
||||
if rinput[2] != View_NUC_SEQS:
|
||||
raise NotImplementedError('obi alignpairedend only works on NUC_SEQS views')
|
||||
|
||||
reverse = rinput[1]
|
||||
|
||||
if len(forward) != len(reverse):
|
||||
raise Exception("Error: the number of forward and reverse reads are different")
|
||||
|
||||
entries = [forward, reverse]
|
||||
input_dms_name = [forward.dms.name, reverse.dms.name]
|
||||
input_view_name = [forward.name, reverse.name]
|
||||
|
||||
else:
|
||||
entries = input[1]
|
||||
input_dms_name = [entries.dms.name]
|
||||
input_view_name = [entries.name]
|
||||
|
||||
if two_views:
|
||||
entries_len = len(forward)
|
||||
else:
|
||||
entries_len = len(entries)
|
||||
|
||||
# Open the output
|
||||
output = open_uri(config['obi']['outputURI'],
|
||||
input=False,
|
||||
newviewtype=View_NUC_SEQS)
|
||||
if output is None:
|
||||
raise Exception("Could not create output view")
|
||||
|
||||
view = output[1]
|
||||
|
||||
Column.new_column(view, QUALITY_COLUMN, OBI_QUAL) #TODO output URI quality option?
|
||||
|
||||
if 'smin' in config['alignpairedend']:
|
||||
smin = config['alignpairedend']['smin']
|
||||
else:
|
||||
smin = 0
|
||||
|
||||
# Initialize the progress bar
|
||||
pb = ProgressBar(entries_len, config, seconde=5)
|
||||
|
||||
if config['alignpairedend']['trueali']:
|
||||
kmer_ali = False
|
||||
aligner = buildAlignment
|
||||
else :
|
||||
kmer_ali = True
|
||||
if type(entries) == list:
|
||||
forward = entries[0]
|
||||
reverse = entries[1]
|
||||
aligner = Kmer_similarity(forward, view2=reverse, kmer_size=config['alignpairedend']['kmersize'])
|
||||
else:
|
||||
aligner = Kmer_similarity(entries, column2=entries[REVERSE_SEQ_COLUMN_NAME], qual_column2=entries[REVERSE_QUALITY_COLUMN_NAME], kmer_size=config['alignpairedend']['kmersize'])
|
||||
|
||||
ba = alignmentIterator(entries, aligner)
|
||||
|
||||
i = 0
|
||||
for ali in ba:
|
||||
|
||||
pb(i)
|
||||
|
||||
consensus = view[i]
|
||||
|
||||
if not two_views:
|
||||
seqF = entries[i]
|
||||
else:
|
||||
seqF = forward[i]
|
||||
|
||||
if smin > 0:
|
||||
if (ali.score > smin) :
|
||||
buildConsensus(ali, consensus, seqF)
|
||||
else:
|
||||
if not two_views:
|
||||
seqR = Nuc_Seq(seqF.id, seqF[REVERSE_SEQ_COLUMN_NAME], quality = seqF[REVERSE_QUALITY_COLUMN_NAME])
|
||||
else:
|
||||
seqR = reverse[i]
|
||||
buildJoinedSequence(ali, seqR, consensus, forward=seqF)
|
||||
|
||||
consensus[b"smin"] = smin
|
||||
else:
|
||||
buildConsensus(ali, consensus, seqF)
|
||||
|
||||
if kmer_ali :
|
||||
ali.free()
|
||||
|
||||
i+=1
|
||||
|
||||
pb(i, force=True)
|
||||
print("", file=sys.stderr)
|
||||
|
||||
if kmer_ali :
|
||||
aligner.free()
|
||||
|
||||
# Save command config in View and DMS comments
|
||||
command_line = " ".join(sys.argv[1:])
|
||||
view.write_config(config, "alignpairedend", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
|
||||
output[0].record_command_line(command_line)
|
||||
|
||||
#print("\n\nOutput view:\n````````````", file=sys.stderr)
|
||||
#print(repr(view), file=sys.stderr)
|
||||
|
||||
input[0].close()
|
||||
if two_views:
|
||||
rinput[0].close()
|
||||
output[0].close()
|
||||
|
||||
logger("info", "Done.")
|
||||
|
||||
@ -1,103 +0,0 @@
|
||||
../../../src/obi_lcs.h
|
||||
../../../src/obi_lcs.c
|
||||
../../../src/obierrno.h
|
||||
../../../src/obierrno.c
|
||||
../../../src/upperband.h
|
||||
../../../src/upperband.c
|
||||
../../../src/sse_banded_LCS_alignment.h
|
||||
../../../src/sse_banded_LCS_alignment.c
|
||||
../../../src/obiblob.h
|
||||
../../../src/obiblob.c
|
||||
../../../src/utils.h
|
||||
../../../src/utils.c
|
||||
../../../src/obidms.h
|
||||
../../../src/obidms.c
|
||||
../../../src/libjson/json_utils.h
|
||||
../../../src/libjson/json_utils.c
|
||||
../../../src/libjson/cJSON.h
|
||||
../../../src/libjson/cJSON.c
|
||||
../../../src/obiavl.h
|
||||
../../../src/obiavl.c
|
||||
../../../src/bloom.h
|
||||
../../../src/bloom.c
|
||||
../../../src/crc64.h
|
||||
../../../src/crc64.c
|
||||
../../../src/murmurhash2.h
|
||||
../../../src/murmurhash2.c
|
||||
../../../src/obidmscolumn.h
|
||||
../../../src/obidmscolumn.c
|
||||
../../../src/obitypes.h
|
||||
../../../src/obitypes.c
|
||||
../../../src/obidmscolumndir.h
|
||||
../../../src/obidmscolumndir.c
|
||||
../../../src/obiblob_indexer.h
|
||||
../../../src/obiblob_indexer.c
|
||||
../../../src/obiview.h
|
||||
../../../src/obiview.c
|
||||
../../../src/hashtable.h
|
||||
../../../src/hashtable.c
|
||||
../../../src/linked_list.h
|
||||
../../../src/linked_list.c
|
||||
../../../src/obidmscolumn_array.h
|
||||
../../../src/obidmscolumn_array.c
|
||||
../../../src/obidmscolumn_blob.h
|
||||
../../../src/obidmscolumn_blob.c
|
||||
../../../src/obidmscolumn_idx.h
|
||||
../../../src/obidmscolumn_idx.c
|
||||
../../../src/obidmscolumn_bool.h
|
||||
../../../src/obidmscolumn_bool.c
|
||||
../../../src/obidmscolumn_char.h
|
||||
../../../src/obidmscolumn_char.c
|
||||
../../../src/obidmscolumn_float.h
|
||||
../../../src/obidmscolumn_float.c
|
||||
../../../src/obidmscolumn_int.h
|
||||
../../../src/obidmscolumn_int.c
|
||||
../../../src/obidmscolumn_qual.h
|
||||
../../../src/obidmscolumn_qual.c
|
||||
../../../src/obidmscolumn_seq.h
|
||||
../../../src/obidmscolumn_seq.c
|
||||
../../../src/obidmscolumn_str.h
|
||||
../../../src/obidmscolumn_str.c
|
||||
../../../src/array_indexer.h
|
||||
../../../src/array_indexer.c
|
||||
../../../src/char_str_indexer.h
|
||||
../../../src/char_str_indexer.c
|
||||
../../../src/dna_seq_indexer.h
|
||||
../../../src/dna_seq_indexer.c
|
||||
../../../src/encode.c
|
||||
../../../src/encode.h
|
||||
../../../src/uint8_indexer.c
|
||||
../../../src/uint8_indexer.h
|
||||
../../../src/build_reference_db.c
|
||||
../../../src/build_reference_db.h
|
||||
../../../src/kmer_similarity.c
|
||||
../../../src/kmer_similarity.h
|
||||
../../../src/obi_clean.c
|
||||
../../../src/obi_clean.h
|
||||
../../../src/obi_ecopcr.c
|
||||
../../../src/obi_ecopcr.h
|
||||
../../../src/obi_ecotag.c
|
||||
../../../src/obi_ecotag.h
|
||||
../../../src/obidms_taxonomy.c
|
||||
../../../src/obidms_taxonomy.h
|
||||
../../../src/obilittlebigman.c
|
||||
../../../src/obilittlebigman.h
|
||||
../../../src/_sse.h
|
||||
../../../src/obidebug.h
|
||||
../../../src/libecoPCR/libapat/CODES/dft_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/dna_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/prot_code.h
|
||||
../../../src/libecoPCR/libapat/apat_parse.c
|
||||
../../../src/libecoPCR/libapat/apat_search.c
|
||||
../../../src/libecoPCR/libapat/apat.h
|
||||
../../../src/libecoPCR/libapat/Gmach.h
|
||||
../../../src/libecoPCR/libapat/Gtypes.h
|
||||
../../../src/libecoPCR/libapat/libstki.c
|
||||
../../../src/libecoPCR/libapat/libstki.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.c
|
||||
../../../src/libecoPCR/ecoapat.c
|
||||
../../../src/libecoPCR/ecodna.c
|
||||
../../../src/libecoPCR/ecoError.c
|
||||
../../../src/libecoPCR/ecoMalloc.c
|
||||
../../../src/libecoPCR/ecoPCR.h
|
||||
@ -1,382 +0,0 @@
|
||||
#cython: language_level=3
|
||||
|
||||
from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport
|
||||
from obitools3.dms import DMS
|
||||
from obitools3.dms.view.view cimport View, Line_selection
|
||||
from obitools3.uri.decode import open_uri
|
||||
from obitools3.apps.optiongroups import addMinimalInputOption, addTaxonomyOption, addMinimalOutputOption
|
||||
from obitools3.dms.view import RollbackException
|
||||
from functools import reduce
|
||||
from obitools3.apps.config import logger
|
||||
from obitools3.utils cimport tobytes, str2bytes
|
||||
from obitools3.dms.capi.obiview cimport NUC_SEQUENCE_COLUMN, \
|
||||
ID_COLUMN, \
|
||||
DEFINITION_COLUMN, \
|
||||
QUALITY_COLUMN, \
|
||||
COUNT_COLUMN
|
||||
|
||||
import time
|
||||
import math
|
||||
import sys
|
||||
|
||||
|
||||
__title__="Annotate views with new tags and edit existing annotations"
|
||||
|
||||
|
||||
SPECIAL_COLUMNS = [NUC_SEQUENCE_COLUMN, ID_COLUMN, DEFINITION_COLUMN, QUALITY_COLUMN]
|
||||
|
||||
|
||||
def addOptions(parser):
|
||||
|
||||
addMinimalInputOption(parser)
|
||||
addTaxonomyOption(parser)
|
||||
addMinimalOutputOption(parser)
|
||||
|
||||
group=parser.add_argument_group('obi annotate specific options')
|
||||
|
||||
group.add_argument('--seq-rank', # TODO seq/elt/line???
|
||||
action="store_true",
|
||||
dest="annotate:add_rank",
|
||||
default=False,
|
||||
help="Add a rank attribute to the sequence "
|
||||
"indicating the sequence position in the data.")
|
||||
|
||||
group.add_argument('-R', '--rename-tag',
|
||||
action="append",
|
||||
dest="annotate:rename_tags",
|
||||
metavar="<OLD_NAME:NEW_NAME>",
|
||||
type=str,
|
||||
default=[],
|
||||
help="Change tag name from OLD_NAME to NEW_NAME.")
|
||||
|
||||
group.add_argument('-D', '--delete-tag',
|
||||
action="append",
|
||||
dest="annotate:delete_tags",
|
||||
metavar="<TAG_NAME>",
|
||||
type=str,
|
||||
default=[],
|
||||
help="Delete tag TAG_NAME.")
|
||||
|
||||
group.add_argument('-S', '--set-tag',
|
||||
action="append",
|
||||
dest="annotate:set_tags",
|
||||
metavar="<TAG_NAME:PYTHON_EXPRESSION>",
|
||||
type=str,
|
||||
default=[],
|
||||
help="Add a new tag named TAG_NAME with "
|
||||
"a value computed from PYTHON_EXPRESSION.")
|
||||
|
||||
group.add_argument('--set-identifier',
|
||||
action="store",
|
||||
dest="annotate:set_identifier",
|
||||
metavar="<PYTHON_EXPRESSION>",
|
||||
type=str,
|
||||
default=None,
|
||||
help="Set sequence identifier with "
|
||||
"a value computed from PYTHON_EXPRESSION.")
|
||||
|
||||
group.add_argument('--set-sequence',
|
||||
action="store",
|
||||
dest="annotate:set_sequence",
|
||||
metavar="<PYTHON_EXPRESSION>",
|
||||
type=str,
|
||||
default=None,
|
||||
help="Change the sequence itself with "
|
||||
"a value computed from PYTHON_EXPRESSION.")
|
||||
|
||||
group.add_argument('--set-definition',
|
||||
action="store",
|
||||
dest="annotate:set_definition",
|
||||
metavar="<PYTHON_EXPRESSION>",
|
||||
type=str,
|
||||
default=None,
|
||||
help="Set sequence definition with "
|
||||
"a value computed from PYTHON_EXPRESSION.")
|
||||
|
||||
group.add_argument('--run',
|
||||
action="store",
|
||||
dest="annotate:run",
|
||||
metavar="<PYTHON_EXPRESSION>",
|
||||
type=str,
|
||||
default=None,
|
||||
help="Run a python expression on each element.")
|
||||
|
||||
group.add_argument('-C', '--clear',
|
||||
action="store_true",
|
||||
dest="annotate:clear",
|
||||
default=False,
|
||||
help="Clear all tags except the obligatory ones.")
|
||||
|
||||
group.add_argument('-k','--keep',
|
||||
action='append',
|
||||
dest="annotate:keep",
|
||||
metavar="<TAG>",
|
||||
default=[],
|
||||
type=str,
|
||||
help="Only keep this tag. (Can be specified several times.)")
|
||||
|
||||
group.add_argument('--length',
|
||||
action="store_true",
|
||||
dest="annotate:length",
|
||||
default=False,
|
||||
help="Add 'seq_length' tag with sequence length.")
|
||||
|
||||
group.add_argument('--with-taxon-at-rank',
|
||||
action='append',
|
||||
dest="annotate:taxon_at_rank",
|
||||
metavar="<RANK_NAME>",
|
||||
default=[],
|
||||
type=str,
|
||||
help="Add taxonomy annotation at the specified rank level RANK_NAME.")
|
||||
|
||||
|
||||
def sequenceTaggerGenerator(config, taxo=None):
|
||||
|
||||
toSet=None
|
||||
newId=None
|
||||
newDef=None
|
||||
newSeq=None
|
||||
length=None
|
||||
add_rank=None
|
||||
run=None
|
||||
|
||||
if 'set_tags' in config['annotate']: # TODO default option problem, to fix
|
||||
toSet = [x.split(':',1) for x in config['annotate']['set_tags'] if len(x.split(':',1))==2]
|
||||
if 'set_identifier' in config['annotate']:
|
||||
newId = config['annotate']['set_identifier']
|
||||
if 'set_definition' in config['annotate']:
|
||||
newDef = config['annotate']['set_definition']
|
||||
if 'set_sequence' in config['annotate']:
|
||||
newSeq = config['annotate']['set_sequence']
|
||||
if 'length' in config['annotate']:
|
||||
length = config['annotate']['length']
|
||||
if 'add_rank' in config["annotate"]:
|
||||
add_rank = config["annotate"]["add_rank"]
|
||||
if 'run' in config['annotate']:
|
||||
run = config['annotate']['run']
|
||||
counter = [0]
|
||||
|
||||
for i in range(len(toSet)):
|
||||
for j in range(len(toSet[i])):
|
||||
toSet[i][j] = tobytes(toSet[i][j])
|
||||
|
||||
annoteRank=[]
|
||||
if config['annotate']['taxon_at_rank']:
|
||||
if taxo is not None:
|
||||
annoteRank = config['annotate']['taxon_at_rank']
|
||||
else:
|
||||
raise Exception("A taxonomy must be provided to annotate taxon ranks")
|
||||
|
||||
def sequenceTagger(seq):
|
||||
|
||||
if counter[0]>=0:
|
||||
counter[0]+=1
|
||||
|
||||
for rank in annoteRank:
|
||||
if 'taxid' in seq:
|
||||
taxid = seq['taxid']
|
||||
if taxid is not None:
|
||||
rtaxid = taxo.get_taxon_at_rank(taxid, rank)
|
||||
if rtaxid is not None:
|
||||
scn = taxo.get_scientific_name(rtaxid)
|
||||
else:
|
||||
scn=None
|
||||
seq[rank]=rtaxid
|
||||
seq["%s_name"%rank]=scn
|
||||
|
||||
if add_rank:
|
||||
seq['seq_rank']=counter[0]
|
||||
|
||||
for i,v in toSet:
|
||||
#try:
|
||||
if taxo is not None:
|
||||
environ = {'taxonomy' : taxo, 'sequence':seq, 'counter':counter[0], 'math':math}
|
||||
else:
|
||||
environ = {'sequence':seq, 'counter':counter[0], 'math':math}
|
||||
val = eval(v, environ, seq)
|
||||
#except Exception,e: # TODO discuss usefulness of this
|
||||
# if options.onlyValid:
|
||||
# raise e
|
||||
# val = v
|
||||
seq[i]=val
|
||||
|
||||
if length:
|
||||
seq['seq_length']=len(seq)
|
||||
|
||||
if newId is not None:
|
||||
# try:
|
||||
if taxo is not None:
|
||||
environ = {'taxonomy' : taxo, 'sequence':seq, 'counter':counter[0], 'math':math}
|
||||
else:
|
||||
environ = {'sequence':seq, 'counter':counter[0], 'math':math}
|
||||
val = eval(newId, environ, seq)
|
||||
# except Exception,e:
|
||||
# if options.onlyValid:
|
||||
# raise e
|
||||
# val = newId
|
||||
seq.id=val
|
||||
|
||||
if newDef is not None:
|
||||
# try:
|
||||
if taxo is not None:
|
||||
environ = {'taxonomy' : taxo, 'sequence':seq, 'counter':counter[0], 'math':math}
|
||||
else:
|
||||
environ = {'sequence':seq, 'counter':counter[0], 'math':math}
|
||||
val = eval(newDef, environ, seq)
|
||||
# except Exception,e:
|
||||
# if options.onlyValid:
|
||||
# raise e
|
||||
# val = newDef
|
||||
seq.definition=val
|
||||
#
|
||||
if newSeq is not None:
|
||||
# try:
|
||||
if taxo is not None:
|
||||
environ = {'taxonomy' : taxo, 'sequence':seq, 'counter':counter[0], 'math':math}
|
||||
else:
|
||||
environ = {'sequence':seq, 'counter':counter[0], 'math':math}
|
||||
val = eval(newSeq, environ, seq)
|
||||
# except Exception,e:
|
||||
# if options.onlyValid:
|
||||
# raise e
|
||||
# val = newSeq
|
||||
seq.seq=val
|
||||
if 'seq_length' in seq:
|
||||
seq['seq_length']=len(seq)
|
||||
# Delete quality since it must match the sequence.
|
||||
# TODO discuss deleting for each sequence separately
|
||||
if QUALITY_COLUMN in seq:
|
||||
seq.view.delete_column(QUALITY_COLUMN)
|
||||
|
||||
if run is not None:
|
||||
# try:
|
||||
if taxo is not None:
|
||||
environ = {'taxonomy' : taxo, 'sequence':seq, 'counter':counter[0], 'math':math}
|
||||
else:
|
||||
environ = {'sequence':seq, 'counter':counter[0], 'math':math}
|
||||
eval(run, environ, seq)
|
||||
# except Exception,e:
|
||||
# if options.onlyValid:
|
||||
# raise e
|
||||
|
||||
return sequenceTagger
|
||||
|
||||
|
||||
def run(config):
|
||||
|
||||
DMS.obi_atexit()
|
||||
|
||||
logger("info", "obi annotate")
|
||||
|
||||
# Open the input
|
||||
input = open_uri(config['obi']['inputURI'])
|
||||
if input is None:
|
||||
raise Exception("Could not read input view")
|
||||
i_dms = input[0]
|
||||
i_view = input[1]
|
||||
i_view_name = input[1].name
|
||||
|
||||
# Open the output: only the DMS, as the output view is going to be created by cloning the input view
|
||||
# (could eventually be done via an open_uri() argument)
|
||||
output = open_uri(config['obi']['outputURI'],
|
||||
input=False,
|
||||
dms_only=True)
|
||||
if output is None:
|
||||
raise Exception("Could not create output view")
|
||||
o_dms = output[0]
|
||||
o_view_name = output[1]
|
||||
|
||||
# If the input and output DMS are not the same, import the input view in the output DMS before cloning it to modify it
|
||||
# (could be the other way around: clone and modify in the input DMS then import the new view in the output DMS)
|
||||
if i_dms != o_dms:
|
||||
imported_view_name = i_view_name
|
||||
i=0
|
||||
while imported_view_name in o_dms: # Making sure view name is unique in output DMS
|
||||
imported_view_name = i_view_name+b"_"+str2bytes(str(i))
|
||||
i+=1
|
||||
View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], i_view_name, imported_view_name)
|
||||
i_view = o_dms[imported_view_name]
|
||||
|
||||
# Clone output view from input view
|
||||
o_view = i_view.clone(o_view_name)
|
||||
if o_view is None:
|
||||
raise Exception("Couldn't create output view")
|
||||
i_view.close()
|
||||
|
||||
# Open taxonomy if there is one
|
||||
if 'taxoURI' in config['obi'] and config['obi']['taxoURI'] is not None:
|
||||
taxo_uri = open_uri(config['obi']['taxoURI'])
|
||||
if taxo_uri is None:
|
||||
raise Exception("Couldn't open taxonomy")
|
||||
taxo = taxo_uri[1]
|
||||
else :
|
||||
taxo = None
|
||||
|
||||
# Initialize the progress bar
|
||||
pb = ProgressBar(len(o_view), config, seconde=5)
|
||||
|
||||
try:
|
||||
|
||||
# Apply editions
|
||||
# Editions at view level
|
||||
if 'delete_tags' in config['annotate']:
|
||||
toDelete = config['annotate']['delete_tags'][:]
|
||||
if 'rename_tags' in config['annotate']:
|
||||
toRename = [x.split(':',1) for x in config['annotate']['rename_tags'] if len(x.split(':',1))==2]
|
||||
if 'clear' in config['annotate']:
|
||||
clear = config['annotate']['clear']
|
||||
if 'keep' in config['annotate']:
|
||||
keep = config['annotate']['keep']
|
||||
for i in range(len(toDelete)):
|
||||
toDelete[i] = tobytes(toDelete[i])
|
||||
for i in range(len(toRename)):
|
||||
for j in range(len(toRename[i])):
|
||||
toRename[i][j] = tobytes(toRename[i][j])
|
||||
for i in range(len(keep)):
|
||||
keep[i] = tobytes(keep[i])
|
||||
keep = set(keep)
|
||||
|
||||
if clear or keep:
|
||||
keys = [k for k in o_view.keys()]
|
||||
for k in keys:
|
||||
if k not in keep and k not in SPECIAL_COLUMNS:
|
||||
o_view.delete_column(k)
|
||||
else:
|
||||
for k in toDelete:
|
||||
o_view.delete_column(k)
|
||||
for old_name, new_name in toRename:
|
||||
if old_name in o_view:
|
||||
o_view.rename_column(old_name, new_name)
|
||||
|
||||
# Editions at line level
|
||||
sequenceTagger = sequenceTaggerGenerator(config, taxo=taxo)
|
||||
for i in range(len(o_view)):
|
||||
pb(i)
|
||||
sequenceTagger(o_view[i])
|
||||
|
||||
except Exception, e:
|
||||
raise RollbackException("obi annotate error, rollbacking view: "+str(e), o_view)
|
||||
|
||||
pb(i, force=True)
|
||||
print("", file=sys.stderr)
|
||||
|
||||
# Save command config in View and DMS comments
|
||||
command_line = " ".join(sys.argv[1:])
|
||||
input_dms_name=[input[0].name]
|
||||
input_view_name=[i_view_name]
|
||||
if 'taxoURI' in config['obi'] and config['obi']['taxoURI'] is not None:
|
||||
input_dms_name.append(config['obi']['taxoURI'].split("/")[-3])
|
||||
input_view_name.append("taxonomy/"+config['obi']['taxoURI'].split("/")[-1])
|
||||
o_view.write_config(config, "annotate", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
|
||||
output[0].record_command_line(command_line)
|
||||
|
||||
#print("\n\nOutput view:\n````````````", file=sys.stderr)
|
||||
#print(repr(o_view), file=sys.stderr)
|
||||
|
||||
# If the input and the output DMS are different, delete the temporary imported view used to create the final view
|
||||
if i_dms != o_dms:
|
||||
View.delete_view(o_dms, imported_view_name)
|
||||
o_dms.close()
|
||||
i_dms.close()
|
||||
|
||||
logger("info", "Done.")
|
||||
@ -1,103 +0,0 @@
|
||||
../../../src/obi_lcs.h
|
||||
../../../src/obi_lcs.c
|
||||
../../../src/obierrno.h
|
||||
../../../src/obierrno.c
|
||||
../../../src/upperband.h
|
||||
../../../src/upperband.c
|
||||
../../../src/sse_banded_LCS_alignment.h
|
||||
../../../src/sse_banded_LCS_alignment.c
|
||||
../../../src/obiblob.h
|
||||
../../../src/obiblob.c
|
||||
../../../src/utils.h
|
||||
../../../src/utils.c
|
||||
../../../src/obidms.h
|
||||
../../../src/obidms.c
|
||||
../../../src/libjson/json_utils.h
|
||||
../../../src/libjson/json_utils.c
|
||||
../../../src/libjson/cJSON.h
|
||||
../../../src/libjson/cJSON.c
|
||||
../../../src/obiavl.h
|
||||
../../../src/obiavl.c
|
||||
../../../src/bloom.h
|
||||
../../../src/bloom.c
|
||||
../../../src/crc64.h
|
||||
../../../src/crc64.c
|
||||
../../../src/murmurhash2.h
|
||||
../../../src/murmurhash2.c
|
||||
../../../src/obidmscolumn.h
|
||||
../../../src/obidmscolumn.c
|
||||
../../../src/obitypes.h
|
||||
../../../src/obitypes.c
|
||||
../../../src/obidmscolumndir.h
|
||||
../../../src/obidmscolumndir.c
|
||||
../../../src/obiblob_indexer.h
|
||||
../../../src/obiblob_indexer.c
|
||||
../../../src/obiview.h
|
||||
../../../src/obiview.c
|
||||
../../../src/hashtable.h
|
||||
../../../src/hashtable.c
|
||||
../../../src/linked_list.h
|
||||
../../../src/linked_list.c
|
||||
../../../src/obidmscolumn_array.h
|
||||
../../../src/obidmscolumn_array.c
|
||||
../../../src/obidmscolumn_blob.h
|
||||
../../../src/obidmscolumn_blob.c
|
||||
../../../src/obidmscolumn_idx.h
|
||||
../../../src/obidmscolumn_idx.c
|
||||
../../../src/obidmscolumn_bool.h
|
||||
../../../src/obidmscolumn_bool.c
|
||||
../../../src/obidmscolumn_char.h
|
||||
../../../src/obidmscolumn_char.c
|
||||
../../../src/obidmscolumn_float.h
|
||||
../../../src/obidmscolumn_float.c
|
||||
../../../src/obidmscolumn_int.h
|
||||
../../../src/obidmscolumn_int.c
|
||||
../../../src/obidmscolumn_qual.h
|
||||
../../../src/obidmscolumn_qual.c
|
||||
../../../src/obidmscolumn_seq.h
|
||||
../../../src/obidmscolumn_seq.c
|
||||
../../../src/obidmscolumn_str.h
|
||||
../../../src/obidmscolumn_str.c
|
||||
../../../src/array_indexer.h
|
||||
../../../src/array_indexer.c
|
||||
../../../src/char_str_indexer.h
|
||||
../../../src/char_str_indexer.c
|
||||
../../../src/dna_seq_indexer.h
|
||||
../../../src/dna_seq_indexer.c
|
||||
../../../src/encode.c
|
||||
../../../src/encode.h
|
||||
../../../src/uint8_indexer.c
|
||||
../../../src/uint8_indexer.h
|
||||
../../../src/build_reference_db.c
|
||||
../../../src/build_reference_db.h
|
||||
../../../src/kmer_similarity.c
|
||||
../../../src/kmer_similarity.h
|
||||
../../../src/obi_clean.c
|
||||
../../../src/obi_clean.h
|
||||
../../../src/obi_ecopcr.c
|
||||
../../../src/obi_ecopcr.h
|
||||
../../../src/obi_ecotag.c
|
||||
../../../src/obi_ecotag.h
|
||||
../../../src/obidms_taxonomy.c
|
||||
../../../src/obidms_taxonomy.h
|
||||
../../../src/obilittlebigman.c
|
||||
../../../src/obilittlebigman.h
|
||||
../../../src/_sse.h
|
||||
../../../src/obidebug.h
|
||||
../../../src/libecoPCR/libapat/CODES/dft_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/dna_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/prot_code.h
|
||||
../../../src/libecoPCR/libapat/apat_parse.c
|
||||
../../../src/libecoPCR/libapat/apat_search.c
|
||||
../../../src/libecoPCR/libapat/apat.h
|
||||
../../../src/libecoPCR/libapat/Gmach.h
|
||||
../../../src/libecoPCR/libapat/Gtypes.h
|
||||
../../../src/libecoPCR/libapat/libstki.c
|
||||
../../../src/libecoPCR/libapat/libstki.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.c
|
||||
../../../src/libecoPCR/ecoapat.c
|
||||
../../../src/libecoPCR/ecodna.c
|
||||
../../../src/libecoPCR/ecoError.c
|
||||
../../../src/libecoPCR/ecoMalloc.c
|
||||
../../../src/libecoPCR/ecoPCR.h
|
||||
@ -1,105 +0,0 @@
|
||||
#cython: language_level=3
|
||||
|
||||
from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport
|
||||
from obitools3.dms.dms cimport DMS
|
||||
from obitools3.dms.view import RollbackException
|
||||
from obitools3.dms.capi.build_reference_db cimport build_reference_db
|
||||
from obitools3.apps.optiongroups import addMinimalInputOption, addTaxonomyOption, addMinimalOutputOption
|
||||
from obitools3.uri.decode import open_uri
|
||||
from obitools3.apps.config import logger
|
||||
from obitools3.utils cimport tobytes, str2bytes
|
||||
from obitools3.dms.view.view cimport View
|
||||
from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS
|
||||
|
||||
import sys
|
||||
|
||||
|
||||
__title__="Tag a set of sequences for PCR and sequencing errors identification"
|
||||
|
||||
|
||||
def addOptions(parser):
|
||||
|
||||
addMinimalInputOption(parser)
|
||||
addTaxonomyOption(parser)
|
||||
addMinimalOutputOption(parser)
|
||||
|
||||
group = parser.add_argument_group('obi build_ref_db specific options')
|
||||
|
||||
group.add_argument('--threshold','-t',
|
||||
action="store", dest="build_ref_db:threshold",
|
||||
metavar='<THRESHOLD>',
|
||||
default=0.0,
|
||||
type=float,
|
||||
help="Score threshold as a normalized identity, e.g. 0.95 for an identity of 95%%. Default: 0.00"
|
||||
" (no threshold).")
|
||||
|
||||
|
||||
def run(config):
|
||||
|
||||
DMS.obi_atexit()
|
||||
|
||||
logger("info", "obi build_ref_db")
|
||||
|
||||
# Open the input: only the DMS
|
||||
input = open_uri(config['obi']['inputURI'],
|
||||
dms_only=True)
|
||||
if input is None:
|
||||
raise Exception("Could not read input")
|
||||
i_dms = input[0]
|
||||
i_dms_name = input[0].name
|
||||
i_view_name = input[1]
|
||||
|
||||
# Open the output: only the DMS
|
||||
output = open_uri(config['obi']['outputURI'],
|
||||
input=False,
|
||||
dms_only=True)
|
||||
if output is None:
|
||||
raise Exception("Could not create output")
|
||||
o_dms = output[0]
|
||||
final_o_view_name = output[1]
|
||||
|
||||
# If the input and output DMS are not the same, build the database creating a temporary view that will be exported to
|
||||
# the right DMS and deleted in the other afterwards.
|
||||
if i_dms != o_dms:
|
||||
temporary_view_name = final_o_view_name
|
||||
i=0
|
||||
while temporary_view_name in i_dms: # Making sure view name is unique in input DMS
|
||||
temporary_view_name = final_o_view_name+b"_"+str2bytes(str(i))
|
||||
i+=1
|
||||
o_view_name = temporary_view_name
|
||||
else:
|
||||
o_view_name = final_o_view_name
|
||||
|
||||
# Read taxonomy name
|
||||
taxonomy_name = config['obi']['taxoURI'].split("/")[-1] # Robust in theory
|
||||
|
||||
# Save command config in View comments
|
||||
command_line = " ".join(sys.argv[1:])
|
||||
input_dms_name=[i_dms_name]
|
||||
input_view_name= [i_view_name]
|
||||
input_dms_name.append(config['obi']['taxoURI'].split("/")[-3])
|
||||
input_view_name.append("taxonomy/"+config['obi']['taxoURI'].split("/")[-1])
|
||||
comments = View.print_config(config, "build_ref_db", command_line, input_dms_name=input_dms_name, input_view_name=input_view_name)
|
||||
|
||||
if build_reference_db(tobytes(i_dms_name), tobytes(i_view_name), tobytes(taxonomy_name), tobytes(o_view_name), comments, config['build_ref_db']['threshold']) < 0:
|
||||
raise Exception("Error building a reference database")
|
||||
|
||||
# If the input and output DMS are not the same, export result view to output DMS
|
||||
if i_dms != o_dms:
|
||||
View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], o_view_name, final_o_view_name)
|
||||
|
||||
# Save command config in DMS comments
|
||||
o_dms.record_command_line(command_line)
|
||||
|
||||
#print("\n\nOutput view:\n````````````", file=sys.stderr)
|
||||
#print(repr(o_dms[final_o_view_name]), file=sys.stderr)
|
||||
|
||||
# If the input and the output DMS are different, delete the temporary result view in the input DMS
|
||||
if i_dms != o_dms:
|
||||
View.delete_view(i_dms, o_view_name)
|
||||
o_dms.close()
|
||||
|
||||
i_dms.close()
|
||||
|
||||
logger("info", "Done.")
|
||||
|
||||
@ -1,103 +0,0 @@
|
||||
../../../src/obi_lcs.h
|
||||
../../../src/obi_lcs.c
|
||||
../../../src/obierrno.h
|
||||
../../../src/obierrno.c
|
||||
../../../src/upperband.h
|
||||
../../../src/upperband.c
|
||||
../../../src/sse_banded_LCS_alignment.h
|
||||
../../../src/sse_banded_LCS_alignment.c
|
||||
../../../src/obiblob.h
|
||||
../../../src/obiblob.c
|
||||
../../../src/utils.h
|
||||
../../../src/utils.c
|
||||
../../../src/obidms.h
|
||||
../../../src/obidms.c
|
||||
../../../src/libjson/json_utils.h
|
||||
../../../src/libjson/json_utils.c
|
||||
../../../src/libjson/cJSON.h
|
||||
../../../src/libjson/cJSON.c
|
||||
../../../src/obiavl.h
|
||||
../../../src/obiavl.c
|
||||
../../../src/bloom.h
|
||||
../../../src/bloom.c
|
||||
../../../src/crc64.h
|
||||
../../../src/crc64.c
|
||||
../../../src/murmurhash2.h
|
||||
../../../src/murmurhash2.c
|
||||
../../../src/obidmscolumn.h
|
||||
../../../src/obidmscolumn.c
|
||||
../../../src/obitypes.h
|
||||
../../../src/obitypes.c
|
||||
../../../src/obidmscolumndir.h
|
||||
../../../src/obidmscolumndir.c
|
||||
../../../src/obiblob_indexer.h
|
||||
../../../src/obiblob_indexer.c
|
||||
../../../src/obiview.h
|
||||
../../../src/obiview.c
|
||||
../../../src/hashtable.h
|
||||
../../../src/hashtable.c
|
||||
../../../src/linked_list.h
|
||||
../../../src/linked_list.c
|
||||
../../../src/obidmscolumn_array.h
|
||||
../../../src/obidmscolumn_array.c
|
||||
../../../src/obidmscolumn_blob.h
|
||||
../../../src/obidmscolumn_blob.c
|
||||
../../../src/obidmscolumn_idx.h
|
||||
../../../src/obidmscolumn_idx.c
|
||||
../../../src/obidmscolumn_bool.h
|
||||
../../../src/obidmscolumn_bool.c
|
||||
../../../src/obidmscolumn_char.h
|
||||
../../../src/obidmscolumn_char.c
|
||||
../../../src/obidmscolumn_float.h
|
||||
../../../src/obidmscolumn_float.c
|
||||
../../../src/obidmscolumn_int.h
|
||||
../../../src/obidmscolumn_int.c
|
||||
../../../src/obidmscolumn_qual.h
|
||||
../../../src/obidmscolumn_qual.c
|
||||
../../../src/obidmscolumn_seq.h
|
||||
../../../src/obidmscolumn_seq.c
|
||||
../../../src/obidmscolumn_str.h
|
||||
../../../src/obidmscolumn_str.c
|
||||
../../../src/array_indexer.h
|
||||
../../../src/array_indexer.c
|
||||
../../../src/char_str_indexer.h
|
||||
../../../src/char_str_indexer.c
|
||||
../../../src/dna_seq_indexer.h
|
||||
../../../src/dna_seq_indexer.c
|
||||
../../../src/encode.c
|
||||
../../../src/encode.h
|
||||
../../../src/uint8_indexer.c
|
||||
../../../src/uint8_indexer.h
|
||||
../../../src/build_reference_db.c
|
||||
../../../src/build_reference_db.h
|
||||
../../../src/kmer_similarity.c
|
||||
../../../src/kmer_similarity.h
|
||||
../../../src/obi_clean.c
|
||||
../../../src/obi_clean.h
|
||||
../../../src/obi_ecopcr.c
|
||||
../../../src/obi_ecopcr.h
|
||||
../../../src/obi_ecotag.c
|
||||
../../../src/obi_ecotag.h
|
||||
../../../src/obidms_taxonomy.c
|
||||
../../../src/obidms_taxonomy.h
|
||||
../../../src/obilittlebigman.c
|
||||
../../../src/obilittlebigman.h
|
||||
../../../src/_sse.h
|
||||
../../../src/obidebug.h
|
||||
../../../src/libecoPCR/libapat/CODES/dft_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/dna_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/prot_code.h
|
||||
../../../src/libecoPCR/libapat/apat_parse.c
|
||||
../../../src/libecoPCR/libapat/apat_search.c
|
||||
../../../src/libecoPCR/libapat/apat.h
|
||||
../../../src/libecoPCR/libapat/Gmach.h
|
||||
../../../src/libecoPCR/libapat/Gtypes.h
|
||||
../../../src/libecoPCR/libapat/libstki.c
|
||||
../../../src/libecoPCR/libapat/libstki.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.c
|
||||
../../../src/libecoPCR/ecoapat.c
|
||||
../../../src/libecoPCR/ecodna.c
|
||||
../../../src/libecoPCR/ecoError.c
|
||||
../../../src/libecoPCR/ecoMalloc.c
|
||||
../../../src/libecoPCR/ecoPCR.h
|
||||
@ -1,124 +0,0 @@
|
||||
#cython: language_level=3
|
||||
|
||||
from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport
|
||||
from obitools3.dms.dms cimport DMS
|
||||
from obitools3.dms.view import RollbackException
|
||||
from obitools3.dms.capi.obiclean cimport obi_clean
|
||||
from obitools3.apps.optiongroups import addMinimalInputOption, addMinimalOutputOption
|
||||
from obitools3.uri.decode import open_uri
|
||||
from obitools3.apps.config import logger
|
||||
from obitools3.utils cimport tobytes, str2bytes
|
||||
from obitools3.dms.view.view cimport View
|
||||
from obitools3.dms.view.typed_view.view_NUC_SEQS cimport View_NUC_SEQS
|
||||
|
||||
import sys
|
||||
|
||||
|
||||
__title__="Tag a set of sequences for PCR and sequencing errors identification"
|
||||
|
||||
|
||||
def addOptions(parser):
|
||||
|
||||
addMinimalInputOption(parser)
|
||||
addMinimalOutputOption(parser)
|
||||
|
||||
group = parser.add_argument_group('obi clean specific options')
|
||||
|
||||
group.add_argument('--distance', '-d',
|
||||
action="store", dest="clean:distance",
|
||||
metavar='<DISTANCE>',
|
||||
default=1.0,
|
||||
type=float,
|
||||
help="Maximum numbers of errors between two variant sequences. Default: 1.")
|
||||
|
||||
group.add_argument('--sample-tag', '-s',
|
||||
action="store",
|
||||
dest="clean:sample-tag-name",
|
||||
metavar="<SAMPLE TAG NAME>",
|
||||
type=str,
|
||||
default="merged_sample",
|
||||
help="Name of the tag where sample counts are kept.")
|
||||
|
||||
group.add_argument('--ratio', '-r',
|
||||
action="store", dest="clean:ratio",
|
||||
metavar='<RATIO>',
|
||||
default=0.5,
|
||||
type=float,
|
||||
help="Maximum ratio between the counts of two sequences so that the less abundant one can be considered"
|
||||
" a variant of the more abundant one. Default: 0.5.")
|
||||
|
||||
group.add_argument('--heads-only', '-H',
|
||||
action="store_true",
|
||||
dest="clean:heads-only",
|
||||
default=False,
|
||||
help="Only sequences labeled as heads are kept in the output. Default: False")
|
||||
|
||||
group.add_argument('--cluster-tags', '-C',
|
||||
action="store_true",
|
||||
dest="clean:cluster-tags",
|
||||
default=False,
|
||||
help="Adds tags for each sequence giving its cluster's head and weight for each sample.")
|
||||
|
||||
|
||||
def run(config):
|
||||
|
||||
DMS.obi_atexit()
|
||||
|
||||
logger("info", "obi clean")
|
||||
|
||||
# Open the input: only the DMS
|
||||
input = open_uri(config['obi']['inputURI'],
|
||||
dms_only=True)
|
||||
if input is None:
|
||||
raise Exception("Could not read input")
|
||||
i_dms = input[0]
|
||||
i_dms_name = input[0].name
|
||||
i_view_name = input[1]
|
||||
|
||||
# Open the output: only the DMS
|
||||
output = open_uri(config['obi']['outputURI'],
|
||||
input=False,
|
||||
dms_only=True)
|
||||
if output is None:
|
||||
raise Exception("Could not create output")
|
||||
o_dms = output[0]
|
||||
final_o_view_name = output[1]
|
||||
|
||||
# If the input and output DMS are not the same, run obiclean creating a temporary view that will be exported to
|
||||
# the right DMS and deleted in the other afterwards.
|
||||
if i_dms != o_dms:
|
||||
temporary_view_name = final_o_view_name
|
||||
i=0
|
||||
while temporary_view_name in i_dms: # Making sure view name is unique in input DMS
|
||||
temporary_view_name = final_o_view_name+b"_"+str2bytes(str(i))
|
||||
i+=1
|
||||
o_view_name = temporary_view_name
|
||||
else:
|
||||
o_view_name = final_o_view_name
|
||||
|
||||
# Save command config in View comments
|
||||
command_line = " ".join(sys.argv[1:])
|
||||
comments = View.print_config(config, "clean", command_line, input_dms_name=[i_dms_name], input_view_name=[i_view_name])
|
||||
|
||||
if obi_clean(tobytes(i_dms_name), tobytes(i_view_name), tobytes(config['clean']['sample-tag-name']), tobytes(o_view_name), comments, \
|
||||
config['clean']['distance'], config['clean']['ratio'], config['clean']['heads-only'], 1) < 0:
|
||||
raise Exception("Error running obiclean")
|
||||
|
||||
# If the input and output DMS are not the same, export result view to output DMS
|
||||
if i_dms != o_dms:
|
||||
View.import_view(i_dms.full_path[:-7], o_dms.full_path[:-7], o_view_name, final_o_view_name)
|
||||
|
||||
# Save command config in DMS comments
|
||||
o_dms.record_command_line(command_line)
|
||||
|
||||
#print("\n\nOutput view:\n````````````", file=sys.stderr)
|
||||
#print(repr(o_dms[final_o_view_name]), file=sys.stderr)
|
||||
|
||||
# If the input and the output DMS are different, delete the temporary result view in the input DMS
|
||||
if i_dms != o_dms:
|
||||
View.delete_view(i_dms, o_view_name)
|
||||
o_dms.close()
|
||||
|
||||
i_dms.close()
|
||||
|
||||
logger("info", "Done.")
|
||||
@ -1,103 +0,0 @@
|
||||
../../../src/obi_lcs.h
|
||||
../../../src/obi_lcs.c
|
||||
../../../src/obierrno.h
|
||||
../../../src/obierrno.c
|
||||
../../../src/upperband.h
|
||||
../../../src/upperband.c
|
||||
../../../src/sse_banded_LCS_alignment.h
|
||||
../../../src/sse_banded_LCS_alignment.c
|
||||
../../../src/obiblob.h
|
||||
../../../src/obiblob.c
|
||||
../../../src/utils.h
|
||||
../../../src/utils.c
|
||||
../../../src/obidms.h
|
||||
../../../src/obidms.c
|
||||
../../../src/libjson/json_utils.h
|
||||
../../../src/libjson/json_utils.c
|
||||
../../../src/libjson/cJSON.h
|
||||
../../../src/libjson/cJSON.c
|
||||
../../../src/obiavl.h
|
||||
../../../src/obiavl.c
|
||||
../../../src/bloom.h
|
||||
../../../src/bloom.c
|
||||
../../../src/crc64.h
|
||||
../../../src/crc64.c
|
||||
../../../src/murmurhash2.h
|
||||
../../../src/murmurhash2.c
|
||||
../../../src/obidmscolumn.h
|
||||
../../../src/obidmscolumn.c
|
||||
../../../src/obitypes.h
|
||||
../../../src/obitypes.c
|
||||
../../../src/obidmscolumndir.h
|
||||
../../../src/obidmscolumndir.c
|
||||
../../../src/obiblob_indexer.h
|
||||
../../../src/obiblob_indexer.c
|
||||
../../../src/obiview.h
|
||||
../../../src/obiview.c
|
||||
../../../src/hashtable.h
|
||||
../../../src/hashtable.c
|
||||
../../../src/linked_list.h
|
||||
../../../src/linked_list.c
|
||||
../../../src/obidmscolumn_array.h
|
||||
../../../src/obidmscolumn_array.c
|
||||
../../../src/obidmscolumn_blob.h
|
||||
../../../src/obidmscolumn_blob.c
|
||||
../../../src/obidmscolumn_idx.h
|
||||
../../../src/obidmscolumn_idx.c
|
||||
../../../src/obidmscolumn_bool.h
|
||||
../../../src/obidmscolumn_bool.c
|
||||
../../../src/obidmscolumn_char.h
|
||||
../../../src/obidmscolumn_char.c
|
||||
../../../src/obidmscolumn_float.h
|
||||
../../../src/obidmscolumn_float.c
|
||||
../../../src/obidmscolumn_int.h
|
||||
../../../src/obidmscolumn_int.c
|
||||
../../../src/obidmscolumn_qual.h
|
||||
../../../src/obidmscolumn_qual.c
|
||||
../../../src/obidmscolumn_seq.h
|
||||
../../../src/obidmscolumn_seq.c
|
||||
../../../src/obidmscolumn_str.h
|
||||
../../../src/obidmscolumn_str.c
|
||||
../../../src/array_indexer.h
|
||||
../../../src/array_indexer.c
|
||||
../../../src/char_str_indexer.h
|
||||
../../../src/char_str_indexer.c
|
||||
../../../src/dna_seq_indexer.h
|
||||
../../../src/dna_seq_indexer.c
|
||||
../../../src/encode.c
|
||||
../../../src/encode.h
|
||||
../../../src/uint8_indexer.c
|
||||
../../../src/uint8_indexer.h
|
||||
../../../src/build_reference_db.c
|
||||
../../../src/build_reference_db.h
|
||||
../../../src/kmer_similarity.c
|
||||
../../../src/kmer_similarity.h
|
||||
../../../src/obi_clean.c
|
||||
../../../src/obi_clean.h
|
||||
../../../src/obi_ecopcr.c
|
||||
../../../src/obi_ecopcr.h
|
||||
../../../src/obi_ecotag.c
|
||||
../../../src/obi_ecotag.h
|
||||
../../../src/obidms_taxonomy.c
|
||||
../../../src/obidms_taxonomy.h
|
||||
../../../src/obilittlebigman.c
|
||||
../../../src/obilittlebigman.h
|
||||
../../../src/_sse.h
|
||||
../../../src/obidebug.h
|
||||
../../../src/libecoPCR/libapat/CODES/dft_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/dna_code.h
|
||||
../../../src/libecoPCR/libapat/CODES/prot_code.h
|
||||
../../../src/libecoPCR/libapat/apat_parse.c
|
||||
../../../src/libecoPCR/libapat/apat_search.c
|
||||
../../../src/libecoPCR/libapat/apat.h
|
||||
../../../src/libecoPCR/libapat/Gmach.h
|
||||
../../../src/libecoPCR/libapat/Gtypes.h
|
||||
../../../src/libecoPCR/libapat/libstki.c
|
||||
../../../src/libecoPCR/libapat/libstki.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.h
|
||||
../../../src/libecoPCR/libthermo/nnparams.c
|
||||
../../../src/libecoPCR/ecoapat.c
|
||||
../../../src/libecoPCR/ecodna.c
|
||||
../../../src/libecoPCR/ecoError.c
|
||||
../../../src/libecoPCR/ecoMalloc.c
|
||||
../../../src/libecoPCR/ecoPCR.h
|
||||
44
python/obitools3/commands/count.py
Normal file
44
python/obitools3/commands/count.py
Normal file
@ -0,0 +1,44 @@
|
||||
'''
|
||||
Created on 8 mars 2016
|
||||
|
||||
@author: coissac
|
||||
'''
|
||||
|
||||
from obitools3.apps.progress import ProgressBar # @UnresolvedImport
|
||||
import time
|
||||
|
||||
__title__="Counts sequences in a sequence set"
|
||||
|
||||
|
||||
default_config = { 'countmode' : None
|
||||
}
|
||||
|
||||
def addOptions(parser):
|
||||
parser.add_argument(dest='obi:input', metavar='obi:input',
|
||||
nargs='?',
|
||||
default=None,
|
||||
help='input data set' )
|
||||
|
||||
group=parser.add_argument_group('Obicount specific options')
|
||||
group.add_argument('-s','--sequence',
|
||||
action="store_true", dest="count:sequence",
|
||||
default=False,
|
||||
help="Prints only the number of sequence records."
|
||||
)
|
||||
|
||||
group.add_argument('-a','--all',
|
||||
action="store_true", dest="count:all",
|
||||
default=False,
|
||||
help="Prints only the total count of sequence records (if a sequence has no `count` attribute, its default count is 1) (default: False)."
|
||||
)
|
||||
|
||||
|
||||
|
||||
def run(config):
|
||||
# The code of my command
|
||||
pb = ProgressBar(1000,config,seconde=1)
|
||||
|
||||
for i in range(1,1001):
|
||||
pb(i)
|
||||
time.sleep(0.01)
|
||||
|
||||
@ -1,55 +0,0 @@
|
||||
#cython: language_level=3
|
||||
|
||||
|
||||
from obitools3.uri.decode import open_uri
|
||||
from obitools3.apps.config import logger
|
||||
from obitools3.dms import DMS
|
||||
from obitools3.apps.optiongroups import addMinimalInputOption
|
||||
from obitools3.dms.capi.obiview cimport COUNT_COLUMN
|
||||
|
||||
|
||||
__title__="Counts sequence records"
|
||||
|
||||
|
||||
def addOptions(parser):
|
||||
|
||||
addMinimalInputOption(parser)
|
||||
|
||||
group = parser.add_argument_group('obi count specific options')
|
||||
|
||||
group.add_argument('-s','--sequence',
|
||||
action="store_true", dest="count:sequence",
|
||||
default=False,
|
||||
help="Prints only the number of sequence records.")
|
||||
|
||||
group.add_argument('-a','--all',
|
||||
action="store_true", dest="count:all",
|
||||
default=False,
|
||||
help="Prints only the total count of sequence records (if a sequence has no `count` attribute, its default count is 1) (default: False).")
|
||||
|
||||
|
||||
def run(config):
|
||||
|
||||
DMS.obi_atexit()
|
||||
|
||||
logger("info", "obi count")
|
||||
|
||||
# Open the input
|
||||
input = open_uri(config['obi']['inputURI'])
|
||||
if input is None:
|
||||
raise Exception("Could not read input")
|
||||
entries = input[1]
|
||||
|
||||
count1 = len(entries)
|
||||
count2 = 0
|
||||
|
||||
if COUNT_COLUMN in entries and ((config['count']['sequence'] == config['count']['all']) or (config['count']['all'])) :
|
||||
for e in entries:
|
||||
count2+=e[COUNT_COLUMN]
|
||||
|
||||
if COUNT_COLUMN in entries and (config['count']['sequence'] == config['count']['all']):
|
||||
print(count1,count2)
|
||||
elif COUNT_COLUMN in entries and config['count']['all']:
|
||||
print(count2)
|
||||
else:
|
||||
print(count1)
|
||||
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Reference in New Issue
Block a user