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Commit Graph

467 Commits

Author SHA1 Message Date
Celine Mercier 5c50e5b378 Embryo of code for openMP parallelization of LCS alignment but 
deactivated for now because can't make it compile with cython/clang
 2016-12-20 11:46:58 +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
Celine Mercier 9c71b06117 Removed deprecated TODOs 2016-12-19 14:36:40 +01:00
Celine Mercier 3bf5260174 Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git 2016-12-19 10:31:18 +01:00
Celine Mercier 857a5198e4 Updated `obi lcs` for the LCS alignment of two columns 2016-12-16 19:40:36 +01:00
Celine Mercier 490f5fe6b9 Updated deprecated code in cython API for columns (using line count of 
view instead of column)
 2016-12-16 19:04:21 +01:00
Celine Mercier 191c83aafc Added missing *.cfiles 2016-12-15 15:28:34 +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
Celine Mercier 8afb1644e9 Alignment: API rework. 'obi align' is now 'obi lcs', and the results are 
now written to columns automatically created in the output view, all
optimally handled at the C level.
 2016-12-12 11:58:59 +01:00
Celine Mercier fa4e4ffaff Changed the cython API to create new views so as to have different 
functions for the different cases
 2016-12-07 14:17:57 +01:00
Celine Mercier 936be64c34 Goes with 5e0c9f87 (missing ';' and fixed compilation warnings) 2016-12-05 11:18:29 +01:00
Celine Mercier 852e5488c8 The default element names for columns with multiple elements per line 
are now "O;1;2;...;n"
 2016-12-02 17:54:51 +01:00
Celine Mercier 98d0849653 Sequence alignment: added the possibility to specify the index of the 
sequences to align in a column containing multiple sequences per line (C
level for now)
 2016-11-29 16:15:02 +01:00
Celine Mercier 76a4c6b14e Fixed a bug when cloning a view and checking its type 2016-11-23 11:28:17 +01:00
Celine Mercier 70c49e214a Added the kmer filter to LCS alignments, and now obiblobs containing 
encoded sequences are directly put in int16_t arrays for the alignment
 2016-11-18 16:29:28 +01:00
Celine Mercier 1c71c195fc Goes with a0ebc2d8 2016-11-10 15:01:29 +01:00
Celine Mercier 359578814b Added view type property to OBIView cython class and updated obi export 
to use it
 2016-11-08 17:49:59 +01:00
Celine Mercier 51b23915ca Added properties for Nuc_Seq cython classes (and updated commands using 
them)
 2016-11-08 16:59:32 +01:00
Celine Mercier b5b889c4a2 Fixed the OBI_Nuc_Seq_Stored cython class not being up to date with the 
new properties of its parent class
 2016-11-08 11:26:37 +01:00
Celine Mercier 36ac315125 Fixed bugs with python view type when creating a new view, and a bug 
when trying to guess the obi type of a nucleotide sequence when its type
was bytes
 2016-11-08 11:23:54 +01:00
Celine Mercier 8291693309 obi grep: updated to work with the new line selection class and within 
the local sequence environment, and progress bar functioning
 2016-11-08 11:19:12 +01:00
Celine Mercier 4bc19c3e49 obi export: view type is now checked and progress bar functioning 2016-11-08 11:17:20 +01:00
Celine Mercier 2d2fe5279d Added functions to add new taxa to a taxonomy with handling of 
associated *.ldx files
 2016-11-03 17:59:21 +01:00
Celine Mercier 2504bf0fa9 Added an iterator to the OBI_Taxonomy cython class 2016-11-02 11:08:18 +01:00
Celine Mercier d8a257e711 Taxonomy handling functions in C. Features: read taxdump, read binary 
files, write binary files. Not fully handled yet: *.adx, *.pdx, *.ldx,
merged.dmp and delnodes.dmp files.
 2016-10-27 18:56:11 +02:00
Celine Mercier b63d0fb9fb Added C functions to write .rdx, .tdx, .ndx binary taxonomy files from a 
taxonomy C structure
 2016-10-14 17:03:10 +02:00
Celine Mercier 1b07109e51 Removed deprecated code 2016-10-10 17:01:51 +02:00
Celine Mercier 60ab503a14 Added properties in the OBI_Taxonomy class 2016-10-10 17:01:17 +02:00
Celine Mercier 2dcfdc59fc When a new view is created with a line selection, the view to clone is 
automatically found + compacted redundant code + fixed potential bug
when cloning a NUC_SEQS view by name
 2016-10-06 17:55:18 +02:00
Celine Mercier 399fc2c051 Removed deprecated source files previously used for tests 2016-09-30 17:49:37 +02:00
Celine Mercier 9cd57deca9 Added OBIView_line_selection class to make new line selections 
associated with the view to clone, and improved and renamed method
closing a view
 2016-09-30 17:48:53 +02:00
Celine Mercier d88811ed7d Added a seed option to the obi test command for reproducible tests 2016-09-29 17:34:48 +02:00
Celine Mercier 8c402101e4 Renamed private attributes as _* and removed some deprecated code 2016-09-28 16:56:44 +02:00
Celine Mercier b717e8bb8b Added properties for the OBIView class and cleaned up deprecated code 2016-09-28 14:26:23 +02:00
Celine Mercier 03a2c8ef7c Finished restructuring the OBIDMS_column class properties 2016-09-27 14:16:30 +02:00
Celine Mercier a7f891d1c9 Added a lines_used property to the OBIDS_column class 2016-09-26 18:04:28 +02:00
Celine Mercier bd50b3f972 Added version property to OBIDMS_column class 2016-09-26 17:45:10 +02:00
Celine Mercier 81380363b7 Added original_name property to OBIDMS_column class 2016-09-26 17:31:32 +02:00
Celine Mercier a4b8349274 Added data_type property to OBIDMS_column class 2016-09-26 17:12:20 +02:00
Celine Mercier a474391b27 Added nb_elements_per_line property to OBIDMS_column class 2016-09-26 17:01:13 +02:00
Celine Mercier a0bc45cc92 Added elements_names property to OBIDMS_column class 2016-09-26 16:53:16 +02:00
Celine Mercier 76f89717fe Added alias property to OBIDMS_column cython class 2016-09-26 16:12:48 +02:00
Celine Mercier b408a4f6eb Changed file name limits to adapt to system limits + minor changes 2016-09-22 18:05:07 +02:00