obitools/obitools3
2
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases 66 Wiki Activity
1,194 Commits 18 Branches 66 Tags
837ff1a1ba39474790cf7e6110737bdfaec6b568
Commit Graph
100 Commits
This Branch
This Branch
All Branches
Author SHA1 Message Date
coissac 13adb479d3 Adds an extern qualifier to the keep_running declaration. 2021-02-05 15:59:43 +01:00
coissac dc88181eeb Add a --cobitools3 options to setup.py 2019-04-12 14:55:05 +02:00
coissac 2f60e91d93 Comment the install of the packages 2019-04-12 13:03:53 +02:00
coissac 7ba27b6a99 Ask for python 3.7 2019-04-01 09:08:27 +02:00
coissac d3937e1051 Add the cmakefile to the manifest 2019-04-01 09:01:45 +02:00
coissac 35eeb07f08 Build the C src in build/cobject 2019-04-01 08:52:38 +02:00
coissac 5d842ff7e7 Clean the manifest of old files 2019-03-29 16:58:45 +01:00
coissac 3445579251 remove all the no more needed .cfiles 2019-03-29 16:56:58 +01:00
coissac 995a66b488 Add the new script emplacement 2019-03-29 16:55:23 +01:00
coissac 5007b02cbc cleaning stage 2 2019-03-29 16:46:17 +01:00
coissac cdd5975e8b Cleaning first stage 2019-03-29 16:40:36 +01:00
coissac 0c466046f4 Merge branch 'pip-standard-orig-python' into 'master' 
The new install version based on classical setup.py

See merge request obitools/obitools3!1
 2019-03-29 16:25:01 +01:00
coissac 2774422224 Patch the way of installing the obi main command 2019-03-29 16:21:28 +01:00
coissac bf62960ee8 Add some .ignore files 2019-03-29 15:52:54 +01:00
coissac 9c41b1e9da Move and rename the obi.py script 2019-03-29 15:45:38 +01:00
coissac 3a6d1be795 remove the old distutils 2019-03-29 15:42:45 +01:00
coissac 6c52966033 Switch back to the original python source from the paster branch 2019-03-29 15:24:31 +01:00
coissac 460187970f First version compiling the code correctly 2019-03-29 15:22:10 +01:00
coissac 52b8008bdc Add the location of install 2019-03-29 15:21:30 +01:00
coissac 6b9da38087 patch some relative imports 2019-03-29 15:19:44 +01:00
coissac 14eca43eac Import taxo 2019-03-26 16:17:44 +01:00
coissac 0b4ea49539 Convert relative import an delete cfiles 2019-03-26 16:14:03 +01:00
coissac cd88c37a7e Merge branch 'pip-standard' of git@git.metabarcoding.org:obitools/obitools3.git into pip-standard 2019-03-26 15:54:49 +01:00
coissac 1095a617a3 Patch relative import to absolute 2019-03-26 15:54:33 +01:00
coissac 10ab557259 First version of the simplified setup.py script 2019-03-26 15:40:31 +01:00
coissac 52de6f2717 Update distutils for openmp and new version of pip 2019-02-19 17:30:53 +01:00
coissac 29c56572cf Add cfiles everywhere ;-) 2019-02-19 15:04:30 +01:00
coissac a776e46e6d Add the command name in the log 2017-09-15 14:51:13 +02:00
coissac 4bb071c048 Merge branch 'master' of 
git@git.metabarcoding.org:obitools/obitools3.git

Conflicts:
	python/obitools3/commands/import.pyx
 2017-09-05 08:59:45 +02:00
coissac 5045d0c2e9 xxx 2017-09-05 08:58:07 +02:00
coissac 407f61a408 Add the possibility to create temporary objects like a temporary 
directory and a temporary DMS
 2017-07-28 16:33:19 +02:00
coissac 09ddd74652 Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git 2017-07-28 15:57:01 +02:00
coissac 7c0d882bc9 Patch a bug when creating a DMS not in the current directory. Use the 
basename function to locate the DMS name instead of the loop...
 2017-07-28 15:56:21 +02:00
coissac b9c65a871f Patch decoding of URL 2017-07-28 12:41:28 +02:00
coissac da48a9d1af Patch group of option : types must be callable not a string 2017-07-28 09:36:18 +02:00
coissac fa8f826cdc Cleanup the end of the file 2017-07-27 16:07:39 +02:00
coissac dc91174a5e Complete the input option group functions 2017-07-27 16:06:48 +02:00
coissac ec65f00cf2 Complete the fasta iterator to manage new input options 2017-07-27 16:05:30 +02:00
coissac 8d9cdb4d03 Complete the fastq iterator to manage new input options 2017-07-27 16:05:17 +02:00
coissac 949e5f9baf Make a first full version of the URI decoder 2017-07-27 16:04:31 +02:00
coissac 3c6a05be54 Add option to the default config corresponding to the parsing of the 
inputs
 2017-07-27 16:03:47 +02:00
coissac 8781ecab1f Add a factory checking the file format and returning the correct 
iterator. First version working only with fasta and fastq nucleic
formats
 2017-07-27 16:02:52 +02:00
coissac 0f6ae7dfa6 Options stuff... ;-) 2017-07-25 13:07:03 +02:00
coissac 28259cd88b Beginning of URI decoder -- !!! NOT YET FULLY IMPLEMENTED !!! 2017-07-25 13:05:58 +02:00
coissac b24be84b0a Add a first group of options 2017-07-25 11:14:30 +02:00
coissac 6dccaa0213 Patch the registering function : register_all_column_classes 2017-04-06 15:37:51 +02:00
coissac cf7f2de016 Modify __init__ and close method to deal with registration process 2017-01-10 14:26:16 +01:00
coissac 5122ad52a7 Merge branch 'Eric_new_Python_API' of git@git.metabarcoding.org:obitools/obitools3.git into Eric_new_Python_API 2017-01-10 14:07:50 +01:00
coissac 4b02ba73ac Add the OBIObject concept 2017-01-10 14:07:10 +01:00
coissac 4a1d3167a7 Last change on my branch 2017-01-02 16:46:52 +01:00
coissac 153c22257f Last change on my branch 2017-01-02 16:46:17 +01:00
coissac 2139bfc748 refactoring... 2017-01-02 13:05:22 +01:00
coissac 65f3b16e6d Refactoring ... 2016-12-29 18:22:05 +01:00
coissac 0526386337 first working DMS class 2016-12-27 06:17:45 +01:00
coissac 62caf1346e temporary remove some files 2016-12-26 15:03:24 +01:00
coissac 3ac6e85fb3 Big refactoring 4 2016-12-26 14:58:03 +01:00
coissac 5156f6bb9e Big refactoring 3 2016-12-26 14:18:01 +01:00
coissac e6db2086d5 Big refactoring 2 2016-12-26 13:56:31 +01:00
coissac daacd0df76 Strong refactoring 1 2016-12-26 13:35:31 +01:00
coissac 3cedd00d7f Add register function for column type 2016-12-20 11:13:57 +01:00
coissac 82fbe43980 transfert method to obiviews 2016-12-20 08:18:47 +01:00
coissac d1a972dfcb patch import 2016-12-20 08:15:42 +01:00
coissac f43dc3e3ab separate the obicolumn classes in new files 2016-12-20 08:15:08 +01:00
coissac 04d39c62ab Try for a new API 2016-12-14 08:44:44 +01:00
coissac 06cb7a9a58 Some change in the way to manage access to special items of the 
dictionary like sequence or quality
 2016-12-13 12:49:34 +01:00
coissac fc55fc117d Some cosmetic on the code 2016-12-13 12:48:13 +01:00
coissac 4ef5cb0d87 Move the OBIView_NUC_SEQS class to files _obiview_nuc_seq.pxd and 
_obiview_nuc_seq.pyx to avoid circular inclusion
 2016-12-13 12:46:49 +01:00
coissac fc805e5443 Remove some warnings in the editor 2016-12-13 08:29:22 +01:00
coissac 8d7ef7d3d1 patch the distutils to add the C source directory in the include path. 
This should solve most of the compilation problems related to .h files
located in this directory
 2016-12-13 08:02:09 +01:00
coissac 6adb9eb623 Should solde issue #56 2016-09-19 21:40:40 +02:00
coissac 400a3f9f3d Merge branch 'Eric_version_for_sequence' 
Conflicts:
	python/obitools3/obidms/_obidmscolumn_seq.pyx
 2016-08-04 09:42:42 +02:00
coissac d1d26b9028 Simplify the code 2016-08-04 08:00:54 +02:00
coissac 465ea81c77 Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git 2016-08-03 10:13:47 +02:00
coissac 1e6d6e32e0 Switch to Cython version >= 0.24 2016-08-03 10:13:10 +02:00
coissac ccc877764e Patch a bug in the printing of the progress bar leading to a bus error 
when compiled with some C compilers and Cython >= 0.24
 2016-08-03 10:12:23 +02:00
coissac 8f0462c407 Merge branch 'master' into Eric_version_for_sequence 
Conflicts:
	python/obitools3/obidms/_obidmscolumn_seq.pyx
 2016-08-03 10:09:20 +02:00
coissac 000b9999ad Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git 2016-07-03 09:22:22 +02:00
coissac aff9831c13 Substitute fprintf call by fputs call to conform with the new ubuntu 
compilation rules
 2016-07-03 09:21:56 +02:00
coissac 448fa8d325 first trial for a fasta formater 2016-07-03 09:18:52 +02:00
coissac 6af62d8124 Change a fprintf without argument to a fputs to comply with the new 
default parameter on ubuntu
 2016-07-03 08:25:06 +02:00
coissac bac7ce7184 Start of the implementation of the export methods 2016-06-02 19:10:33 +02:00
coissac f186395661 Trap potential exception generated by char* to bytes casts 2016-05-29 21:18:20 +02:00
coissac 85395dfc1a value returned for sequence is now bytes and no more str 2016-05-29 13:53:32 +02:00
coissac f830389974 Add some comment on the location of the align method. 2016-05-29 12:58:31 +02:00
coissac 2e35229357 Add conversion checking on the value of a seq column 2016-05-29 12:54:13 +02:00
coissac a8ed57dc6e few small changes 2016-05-21 12:29:55 +02:00
coissac c3274d419c remove an extra debug log 2016-05-21 12:29:08 +02:00
coissac cca0dbb46b Close issue #54 by adding a read1 method to the MagicKeyFile class 2016-05-21 12:24:48 +02:00
coissac 5a78157112 increase parsing speed of the header 2016-05-21 10:29:11 +02:00
coissac 0b9a41d952 Patch a bug about the reading of the last sequence 2016-05-21 10:28:03 +02:00
coissac ef1be141c1 Update Licence to english version 2016-04-23 18:03:50 +02:00
coissac bbfd40d56d Add license 2016-04-23 18:03:10 +02:00
coissac 6fe4c6134a Allows for calling getConfiguration without parametter for geting the 
default configuration
 2016-04-11 13:31:09 +02:00
coissac 45c9c5075c A first version of the fasta parser 2016-04-01 18:15:54 +02:00
coissac 20b97c972b Add boolean type in the tag evaluation 2016-04-01 13:42:24 +02:00
coissac efc4a4a3c6 Reduce the call count to eval. This reduce by 3 the time of fast(q|a) 
header processing
 2016-04-01 08:54:06 +02:00
coissac ce6ea89c21 Add the missing bootstrappip module 2016-03-31 17:28:03 +02:00
coissac 4207db7c17 Transfers bug patch from orgasm 2016-03-31 16:53:09 +02:00
coissac 1cd35b3359 firt version of a fastq parser 2016-03-31 10:47:12 +02:00
coissac f51a6df5b2 Add a class buffering lines during a text file reading 2016-03-30 14:53:25 +02:00