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680 Commits 18 Branches 66 Tags
3e8c187f0b1fc177f6c89be2d20e4587343c3f4b
Commit Graph

388 Commits

Author SHA1 Message Date
Celine Mercier
dfd51939a0 Views are now rollbacked if an error occurs, and unfinished views and 
columns are deleted when an OBIDMS is opened.
 2017-10-26 18:58:48 +02:00
Celine Mercier
1ae634d56b Added atexit command to obi import, obi uniq and obi less 2017-10-16 11:09:55 +02:00
Celine Mercier
04e065094a All DMS opened by a program are now listed and closed with atexit system 2017-10-16 10:35:07 +02:00
Celine Mercier
5ddd1d9ae6 obi uniq: added taxonomy handling 2017-10-04 16:13:07 +02:00
Celine Mercier
f2ece573ff Removed deprecated command 2017-10-04 16:09:41 +02:00
Celine Mercier
fb9b219abe Fixed a bug with taxonomy URIs not being read correctly 2017-10-04 16:00:30 +02:00
Celine Mercier
09a5f89849 Column API: improvements to be more flexible when referring to elements 
in columns with several elements per line.
 2017-10-04 15:59:23 +02:00
Celine Mercier
535692b020 Taxonomy: new functions and improvements 2017-10-04 15:55:13 +02:00
Celine Mercier
0ab081f79e Updated obi test to work with changes in taxonomy API 2017-10-04 15:50:32 +02:00
Celine Mercier
1cb05de7e3 Basic obi less 2017-10-04 15:46:26 +02:00
Celine Mercier
532d8e9cd7 obi import: small efficiency improvement when dealing with NA values 2017-10-04 15:44:48 +02:00
Celine Mercier
b4088a7928 Cython API: Added basic taxonomy option 2017-10-04 15:42:17 +02:00
Celine Mercier
ae24a807da obi uniq: added the option to merge ids, except it only works on small 
sets until lists are implemented properly using obiblobs
 2017-09-25 17:28:03 +02:00
Celine Mercier
75c15594c4 obi uniq: added option to use categories additionally to the sequence to 
determine uniqueness
 2017-09-25 10:56:43 +02:00
Celine Mercier
41dec03448 Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git 2017-09-18 16:08:31 +02:00
Eric Coissac
a776e46e6d Add the command name in the log 2017-09-15 14:51:13 +02:00
Celine Mercier
0e140df0fb Cython API: added some imports in __init__ files 2017-09-14 18:30:04 +02:00
Celine Mercier
73bca6288f New obi uniq 2017-08-20 18:04:21 +02:00
Celine Mercier
6a2759eee6 obi import with new input/ouput API 2017-08-20 17:58:36 +02:00
Celine Mercier
663a1a1091 Cython API: column elements: added possibility to check if an element 
exists from its index, and a dict-like get() method
 2017-08-20 17:44:05 +02:00
Celine Mercier
c6d5436a58 Cython API: fixed a bug where iteration on a NUC_SEQS view would not be 
done correctly (bug appeared with optimization modifications done
lately)
 2017-08-20 17:41:41 +02:00
Celine Mercier
47cad285d6 Cython API: fixed 2 little bugs in Seq API 2017-08-20 17:39:30 +02:00
Celine Mercier
74f15d1a23 Cython API: Various fixes in input handlers (parsers, openers etc). 
Mostly working but not bug-free
 2017-08-20 17:37:51 +02:00
Celine Mercier
7f1ff49aa2 Cython API to import a column and a view from a DMS to another DMS 2017-08-03 16:34:02 +02:00
Eric 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
Celine Mercier
35b0c55a8c Cython API: various improvements and checks 2017-07-28 13:15:13 +02:00
Eric Coissac
b9c65a871f Patch decoding of URL 2017-07-28 12:41:28 +02:00
Celine Mercier
84bb93096f Cython API: fixes and improvements in Column API 2017-07-28 10:27:04 +02:00
Celine Mercier
01c69e7e25 Cython API: fixed a bug when printing a column 2017-07-28 10:01:56 +02:00
Celine Mercier
adf5cbef97 Added DMS method to create a DMS if it doesn't already exists, otherwise 
opens it
 2017-07-28 09:55:43 +02:00
Eric Coissac
da48a9d1af Patch group of option : types must be callable not a string 2017-07-28 09:36:18 +02:00
Celine Mercier
9482c663c0 minor comments and changes 2017-07-27 19:46:34 +02:00
Celine Mercier
89e2f80fd8 Goes with previous commit 2017-07-27 19:43:00 +02:00
Celine Mercier
7112f44fb7 Bug fixes for input handlers, openers, parsers etc. Compiling but not 
tested
 2017-07-27 19:42:44 +02:00
Celine Mercier
b2fc1f4611 obi uniq: first version 2017-07-27 19:40:19 +02:00
Celine Mercier
75f691d55a Cython API: Seq classes reworked 2017-07-27 19:39:58 +02:00
Celine Mercier
0655063bb0 Cython API: view_NUC_SEQS changes to go with previous commits 2017-07-27 19:39:26 +02:00
Celine Mercier
9701b1230c Cython API: OBIWrapper.new method is now OBIWrapper.new_wrapper to avoid 
mismatching method definitions with subclasses
 2017-07-27 19:38:25 +02:00
Celine Mercier
f8a4428674 Cython API: DMS test_open method doesn't raise an exception anymore 2017-07-27 19:36:28 +02:00
Celine Mercier
1a0f18a11a Cython API: added a __setitem__ method to the View class that can detect 
if the item is a Line and create the corresponding columns if needed +
minor changes
 2017-07-27 19:35:28 +02:00
Celine Mercier
3d7aa52c90 Cython API: Fixed a bug when setting NA values in Column_multi_elts, and 
added some properties
 2017-07-27 19:31:15 +02:00
Celine Mercier
69c50ff922 Cython API: added a Column subclass to allow direct access to indexes 
for columns that store indexes referring to other data
 2017-07-27 19:29:10 +02:00
Celine Mercier
c91969126b Cython C API declarations to go with previous commit 2017-07-27 19:26:59 +02:00
Celine Mercier
15d383fa8b Added possibility to specify the offset for encoding and decoding 
sequence quality character strings
 2017-07-27 19:24:41 +02:00
Celine Mercier
99ceed5fff Cython API: renamed OBI_Taxonomy to Taxonomy and OBI_Taxon to Taxon 2017-07-27 19:21:45 +02:00
Eric Coissac
fa8f826cdc Cleanup the end of the file 2017-07-27 16:07:39 +02:00
Eric Coissac
dc91174a5e Complete the input option group functions 2017-07-27 16:06:48 +02:00
Eric Coissac
ec65f00cf2 Complete the fasta iterator to manage new input options 2017-07-27 16:05:30 +02:00
Eric Coissac
8d9cdb4d03 Complete the fastq iterator to manage new input options 2017-07-27 16:05:17 +02:00
Eric Coissac
949e5f9baf Make a first full version of the URI decoder 2017-07-27 16:04:31 +02:00