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Cleaning of the doc, more stuff...

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This commit is contained in:
Eric Coissac
2013-12-24 14:27:03 +00:00
parent 4fe1c167ef
commit 5537714c08
8 changed files with 37 additions and 20 deletions
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6
doc/sphinx/source/optionsSet/sequenceFilter.txt
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@ -73,7 +73,8 @@ Sequence record selection options
Keeps only the sequence records whose identifier is present in the
``my_id_list.txt`` file.
.. cmdoption:: -a <ATTRIBUTE_NAME>:<REGULAR_PATTERN>, --attribute=<ATTRIBUTE_NAME>:<REGULAR_PATTERN>
.. cmdoption:: -a <ATTRIBUTE_NAME>:<REGULAR_PATTERN>,
.. cmdoption:: --attribute=<ATTRIBUTE_NAME>:<REGULAR_PATTERN>
Regular expression pattern matched against the
:doc:`attributes of the sequence record <../fasta>`. the value of this attribute
@ -120,7 +121,8 @@ Sequence record selection options
.. code-block:: bash
> obigrep -p '(forward_error<2) and (reverse_error<2)' seq1.fasta > seq2.fasta
> obigrep -p '(forward_error<2) and (reverse_error<2)' \
seq1.fasta > seq2.fasta
Keeps only the sequence records whose ``forward_error`` and ``reverse_error``
attributes have a value smaller than two.

6
doc/sphinx/source/scripts/ecoPCR.rst
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@ -146,7 +146,8 @@ Examples
.. code-block:: bash
> ecoPCR -d mydatabase -e 3 -l 50 -L 500 TCACAGACCTGTTATTGC TYTGTCTGSTTRATTSCG > mysequences.ecopcr
> ecoPCR -d mydatabase -e 3 -l 50 -L 500 \
TCACAGACCTGTTATTGC TYTGTCTGSTTRATTSCG > mysequences.ecopcr
Launches an *in silico* PCR on mydatabase (in the ``ecoPCR format``, see :py:mod:`obiconvert`),
with a maximum of three mismatches for each primer. The minimum and maximum amplified sequence
@ -161,7 +162,8 @@ Examples
.. code-block:: bash
> ecoPCR -d mydatabase -e 2 -l 80 -L 120 -D 50 -r 7742 TTAGATACCCCACTATG#C# TAGAACAGGCTCCTCTA#G# > mysequences.ecopcr
> ecoPCR -d mydatabase -e 2 -l 80 -L 120 -D 50 -r 7742 \
TTAGATACCCCACTATG#C# TAGAACAGGCTCCTCTA#G# > mysequences.ecopcr
Launches an *in silico* PCR on mydatabase (in the ``ecoPCR format``, see :py:mod:`obiconvert`),
with a maximum of two mismatches for each primer, but with a perfect match on the last two nucleotides

6
doc/sphinx/source/scripts/ecoPrimers.rst
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@ -210,7 +210,8 @@ Examples
.. code-block:: bash
> ecoPrimers -d mydatabase -e 3 -l 50 -L 800 -r 2759 -3 2 > mybarcodes.ecoprimers
> ecoPrimers -d mydatabase -e 3 -l 50 \
-L 800 -r 2759 -3 2 > mybarcodes.ecoprimers
Launches a search for barcodes and corresponding primers on mydatabase (in the ``ecoPCR format``,
see :py:mod:`obiconvert`), with a maximum of three mismatches for each primer. The minimum and
@ -225,7 +226,8 @@ Examples
.. code-block:: bash
> ecoPrimers -d mydatabase -e 2 -l 30 -L 120 -r 7742 - i 2 -E 9604 -3 2 > mybarcodes.ecoprimers
> ecoPrimers -d mydatabase -e 2 -l 30 -L 120 \
-r 7742 - i 2 -E 9604 -3 2 > mybarcodes.ecoprimers
Launches a search for barcodes and corresponding primers on mydatabase (in the `ecoPCR format`,
see :py:mod:`obiconvert`), with a maximum of two mismatches for each primer. The minimum and

3
doc/sphinx/source/scripts/obiconvert.rst
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@ -4,7 +4,8 @@
.. code-block:: bash
> obiconvert --ecopcrdb --fasta-output 'my_ecopcr_database' > sequences.fasta
> obiconvert --ecopcrdb --fasta-output \
'my_ecopcr_database' > sequences.fasta
Converts an ecopcr database in a sequence file in *extended OBITools fasta* format.

15
doc/sphinx/source/scripts/obitaxonomy.rst
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@ -15,7 +15,8 @@
.. code-block:: bash
> obitaxonomy -d my_ecopcr_database -a 'Gentiana alpina':'species':21496
> obitaxonomy -d my_ecopcr_database \
-a 'Gentiana alpina':'species':21496
Adds a taxon with the scientific name *Gentiana alpina* and the rank *species* under
the taxon whose taxid is 21496.
@ -29,7 +30,8 @@
.. code-block:: bash
> obitaxonomy -d my_ecopcr_database -m 1000000000 -a 'Gentiana alpina':'species':21496
> obitaxonomy -d my_ecopcr_database -m 1000000000 \
-a 'Gentiana alpina':'species':21496
Adds a taxon with the scientific name *Gentiana alpina* and the rank *species* under
the taxon whose taxid is 21496, with a taxid greater than or equal to 1000000000.
@ -75,7 +77,8 @@
.. code-block:: bash
> obitaxonomy -d my_ecopcr_database -f 'Gentiana algida':10000832
> obitaxonomy -d my_ecopcr_database \
-f 'Gentiana algida':10000832
Adds the favorite scientific name *Gentiana algida* for the taxid 10000832 in the taxonomic database.
@ -91,7 +94,8 @@
.. code-block:: bash
> obitaxonomy -d my_ecopcr_database -k my_taxon_name_key -F my_sequences.fasta
> obitaxonomy -d my_ecopcr_database \
-k my_taxon_name_key -F my_sequences.fasta
Adds the taxon of each sequence record from the file ``my_sequences.fasta`` in the taxonomic
database, based on the scientific name contained in the ``my_taxon_name_key`` attribute.
@ -120,7 +124,8 @@
.. code-block:: bash
> obitaxonomy -d my_ecopcr_database -a 33090 -k my_taxon_name_key -F my_sequences.fasta
> obitaxonomy -d my_ecopcr_database -a 33090 \
-k my_taxon_name_key -F my_sequences.fasta
Adds the taxon of each sequence record from the file ``my_sequences.fasta`` in the taxonomic
database, based on the scientific name contained in the ``my_taxon_name_key`` attribute. If

3
src/ecotag.py
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@ -24,7 +24,8 @@ for each taxid.
.. code-block:: bash
> ecotag -d embl_r113 -R ReferenceDB.fasta --sort=count -m 0.95 -r seq.fasta > seq_tag.fasta
> ecotag -d embl_r113 -R ReferenceDB.fasta \\
--sort=count -m 0.95 -r seq.fasta > seq_tag.fasta
The above command specifies that each sequence stored in ``seq.fasta``
is compared to those in the reference database called ``ReferenceDB.fasta``

18
src/obiannotate.py
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@ -12,7 +12,7 @@ annotation attributes attached to sequence records.
Once such attributes are added, they can be used by the other OBITools commands for
filtering purposes or for statistics computing.
*Example:*
*Example 1:*
.. code-block:: bash
@ -20,31 +20,35 @@ filtering purposes or for statistics computing.
The above command adds an attribute named *short* which has a boolean value indicating whether the sequence length is less than 100bp.
*Example:*
*Example 2:*
.. code-block:: bash
> obiannotate --rank seq1.fasta | obiannotate -C --set-identifier '"'FungA'_%05d" % seq_rank' > seq2.fasta
> obiannotate --rank seq1.fasta | \\
obiannotate -C --set-identifier '"'FungA'_%05d" % seq_rank' \\
> seq2.fasta
The above command adds a new attribute whose value is the sequence record
entry number in the file. Then it clears all the sequence record attributes
and sets the identifier to a string beginning with *FungA_* followed by a
suffix with 5 digits containing the sequence entry number.
*Example:*
*Example 3:*
.. code-block:: bash
> obiannotate -d my_ecopcr_database --with-taxon-at-rank=genus seq1.fasta > se2.fasta
> obiannotate -d my_ecopcr_database \\
--with-taxon-at-rank=genus seq1.fasta > seq2.fasta
The above command adds taxonomic information at the *genus* rank to the
sequence records.
*Example:*
*Example 4:*
.. code-block:: bash
> obiannotate -S 'new_seq:str(sequence).replace("a","t")' seq1.fasta | obiannotate --set-sequence new_seq > seq2.fasta
> obiannotate -S 'new_seq:str(sequence).replace("a","t")' \\
seq1.fasta | obiannotate --set-sequence new_seq > seq2.fasta
The overall aim of the above command is to edit the *sequence* object itself,
by replacing all nucleotides *a* by nucleotides *t*. First, a new attribute