obitools/obitools3
2
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases 66 Wiki Activity
805 Commits 18 Branches 66 Tags
d88390c6d8542a06b6b8a23a02ddeb9dc812ee3b
Commit Graph
100 Commits
This Branch
This Branch
All Branches
Author SHA1 Message Date
Celine Mercier d88390c6d8 Cython API: when importing a file in a DMS, its length is computed 
beforehand for the progress bar
 2019-03-13 18:35:32 +01:00
Celine Mercier 50e7cd61a6 added math.h import where needed 2019-03-13 11:17:25 +01:00
Celine Mercier 49d5f6fb1e removed deprecated comment 2019-03-13 11:17:04 +01:00
Celine Mercier b45c2ee653 Cython API: cleaner column rewriting API 2019-03-13 11:13:55 +01:00
Celine Mercier 6afd1294a7 Cython API: Views: fixed a bug when rewriting a column with different 
attributes (last line is not written anymore)
 2019-03-12 16:40:30 +01:00
Celine Mercier 185a95e667 cleaner Makefile 2019-03-11 15:20:10 +01:00
Celine Mercier 8835a1a983 removed -R compilaiton flag that gcc doesn't like 2019-03-07 15:55:46 +01:00
Celine Mercier 1ee50b7222 Fixed a bug when creating a column and checking the comments string if 
it was NULL
 2019-03-07 15:09:59 +01:00
Celine Mercier 720bb65b24 Installation: basic Makefile that creates the shared obi3 library used 
by Cython
 2019-03-07 14:01:37 +01:00
Celine Mercier 2a1ab9db29 Cython API, Views: guessing an obitype from a python value is now done 
through the corresponding functions in utils
 2019-03-07 13:57:37 +01:00
Celine Mercier 4bc52c08c2 minor changes 2019-03-07 13:53:37 +01:00
Celine Mercier 306da846e3 obidistutils: link obi3 C shared library instead of compiling all C 
files with all modules (creating issues with global/static variables).
EXCEPT RUNTIME LINKING DOESN'T WORK YET
 2019-03-07 13:50:29 +01:00
Celine Mercier af57e532da obidistutils: create doc/sphinx dir if needed 2019-03-07 13:47:23 +01:00
Celine Mercier de3d12af17 Renamed CAPI file 2019-02-19 14:50:30 +01:00
Celine Mercier 9ccddd5280 better cfiles 2019-02-19 14:11:29 +01:00
Celine Mercier e026e9ec83 Fixed the new alignpaired end to work after ngsfilter with the 9879847 
possible cases
 2019-02-17 18:32:35 +01:00
Celine Mercier 4ddd1a1c37 embl iterator: only option on embl directories now works as intended 2019-02-12 16:46:08 +01:00
Celine Mercier 3015310535 Fixed a bug in kmer similarity computation where the fact that sequences 
could be switched was not accounted for
 2019-02-10 21:02:24 +01:00
Celine Mercier 08bcbcd357 ngsfilter: reworked to use apat library 2019-02-06 18:13:54 +01:00
Celine Mercier 04a3682307 Cython API: added API to use apat (pattern search) C library 2019-02-06 18:12:49 +01:00
Celine Mercier 6ca6d27ecb ecoPCR: fixed amplicon length computation bug 2019-02-06 18:11:20 +01:00
Celine Mercier 8f18907566 Cython API: changed revcomp attribute of Nuc_Seq class to is_revcomp to 
be more explicit
 2019-02-06 18:09:11 +01:00
Celine Mercier 0b62619e4e Various commentaries and insignificant fixes 2019-01-21 17:32:44 +01:00
Celine Mercier c7f5b8d980 Alignpairedend: added alignment using shifting with best kmer similarity 
(low level layer in C and Cython API)
 2019-01-21 17:30:46 +01:00
Celine Mercier 59017c0d6b C: taxonomy: fixed a bug when checking for root node 2019-01-21 17:23:25 +01:00
Celine Mercier 9f6bba183f C: Added a function to get a nucleotide at a specific index in an 
encoded sequence
 2019-01-21 17:18:02 +01:00
Celine Mercier 2a6a112d29 obi import: fixed writing quality in views when appropriate (but still 
not a satisfying solution)
 2018-12-11 19:33:55 +01:00
Celine Mercier c437931a35 Cython: fixed history dot graph for all views, and fixed history 
recording for build_ref_db and ecotag
 2018-12-10 17:09:00 +01:00
Celine Mercier eb586b2f53 New command and C functions: obi ecotag 2018-12-09 19:19:32 +01:00
Celine Mercier 9556130b11 C obi_lcs: updated deprecated column names and associated comments 2018-12-09 19:17:13 +01:00
Celine Mercier 005aaeec06 C obi_lcs: fixed checking for identical sequences when aligning 2 
columns
 2018-12-09 19:16:44 +01:00
Celine Mercier 579f56bb54 obi align (pouic): fixed bug with the saved config when aligning 2 
different views
 2018-12-09 19:15:58 +01:00
Celine Mercier da445066f3 C alignment filter: added a check for sequences not being equal when the 
threshold requires that they are
 2018-12-09 19:14:51 +01:00
Celine Mercier 0a407436da C Views: made an error message more specific 2018-12-09 19:14:05 +01:00
Celine Mercier 54efff36c4 C build ref db: fixed 2 bugs when setting arrays: size of an element in 
in bits not bytes and using view API instead of column API
 2018-12-09 19:13:06 +01:00
Celine Mercier 6acb21712a Missing commit for build_ref_db: C API file for cython 2018-12-09 19:11:59 +01:00
Celine Mercier 12087a6c3a C, views: made 'view_exists' function public (now 'obi_view_exists') 2018-11-27 16:20:30 +01:00
Celine Mercier fbabbceb5a Fixed a bug in the array indexer where the value's length was no 
properly set to 0 if the value was NA (ignore previous commit with the
same message)
 2018-11-27 16:18:34 +01:00
Celine Mercier 6f27734d71 Cython: fxed a bug in INT tuple columns where values were converted to 
double instead of int
 2018-11-27 16:14:56 +01:00
Celine Mercier b3bfa9ca65 Fixed a bug in the array indexer where the value's length was not 
properly set to 0 if the value was NA
 2018-11-27 16:12:41 +01:00
Celine Mercier ece942e771 new command: build_ref_db to build a reference database with metadata 
for the taxonomic assignment of sequences
 2018-11-27 16:11:18 +01:00
Celine Mercier ef8dc85f3c C, taxonomy: new function to get the lowest common ancestor of two taxa 2018-11-27 16:00:29 +01:00
Celine Mercier f942dd856f C: new function to build a reference database with LCA and score 
metadata for the taxonomic assignment of sequences
 2018-11-27 15:56:50 +01:00
Celine Mercier 730ea99f85 minor fixes and comments 2018-11-19 11:23:54 +01:00
Celine Mercier 4d51f4f015 obi import: better checking of whether to import quality 2018-11-19 11:23:39 +01:00
Celine Mercier e9c1d5e48d AVLs: made maximum number of nodes per AVL 5 millions, as this combined 
with keeping all AVLs mapped seems the most efficient. Now 1 million
sequences more or less constantly takes 1 minute.
 2018-11-19 11:22:26 +01:00
Celine Mercier 7fc1b578cf AVLs: AVLs in a group are not unmapped and remapped constantly anymore 
when adding new values, fixed a bug when calculating if an AVL data file
has reached the maximum size, fixed a casting bug, and added a boolean
so read-only AVLs files are not truncated
 2018-11-19 11:19:07 +01:00
Celine Mercier 31053591b5 Fixed 2 bugs when checking qualities matching sequences predicate: now 
closing and reopening indexers so that they are mapped properly, and
fixed memory leak when reading sequences
 2018-11-19 11:05:53 +01:00
Celine Mercier b0da36cb48 New command: obi align, except it's called obi pouic for now because of 
a Cython compilation bug
 2018-11-07 16:05:48 +01:00
Celine Mercier d1f1fd432e Minor fixes 2018-11-07 16:04:17 +01:00
Celine Mercier 75a28929a7 Renamed Cython alignment library in an attempt to limit some compilation 
bugs potentially involving name conflicts
 2018-11-07 16:03:32 +01:00
Celine Mercier d076ea9900 Alignment: updated functions to align columns (LCS) 2018-11-07 16:00:58 +01:00
Celine Mercier 6b1c41f3fb Changed an error message to be more specific 2018-11-07 13:37:25 +01:00
Celine Mercier 362df50fe9 Removed a deprecated element from the DMS structure 2018-11-07 13:36:08 +01:00
Celine Mercier b1090574da View import: associated column informations are now correctly updated 
with the new versions
 2018-11-07 13:35:11 +01:00
Celine Mercier 8faabd3ebf Cython, URI: Fixed a bug when using an output URI with just a view name 
to use the default DMS
 2018-11-02 19:04:27 +01:00
Celine Mercier 35f3e7c30b All commands now handle outputing to another DMS + small fixes 2018-11-02 19:03:09 +01:00
Celine Mercier 8a8e9e50b2 Fixed declaration going with previous commit 2018-10-31 18:01:04 +01:00
Celine Mercier c7ff53b948 obi clean: temporary views are now deleted 2018-10-31 17:52:51 +01:00
Celine Mercier 1b7bccb236 Small improvement when checking if a view exists 2018-10-31 17:51:10 +01:00
Celine Mercier d09aa43133 Cython API: added a function to get the full path to the DMS directory 2018-10-31 14:46:25 +01:00
Celine Mercier 123e5dc0ac Cython URI API: added an argument to only open the DMS and return the 
rest as a character string
 2018-10-31 14:45:17 +01:00
Celine Mercier 320561a582 Views: Added argument to not automatically create default columns in 
typed views, a function to delete a view and fixed view history bug
 2018-10-31 14:38:05 +01:00
Celine Mercier 92c0fbc9bf Fixed a bug where an imported column was not flagged as finished, 
resulting in its deletion when reopening the DMS.
 2018-10-29 17:39:30 +01:00
Celine Mercier b11d52d630 Fixed a bug with the DMS counter being wrongly initialized to 0 instead 
of 1 (generating memory bugs when using the counter)
 2018-10-29 16:12:37 +01:00
Celine Mercier 6305282305 obi clean: made more efficient with arrays (speed ~x15 compared with 
OBI1)
 2018-10-21 17:59:02 +02:00
Celine Mercier d53323e7f4 Fixed comments bug with obi head and obi tail 2018-10-21 17:39:17 +02:00
Celine Mercier e18b762d81 Weird buggy Eclipse commit with nothing changed 2018-10-21 17:35:18 +02:00
Celine Mercier 0a0f0682a9 Better handling of errors and exceptions when new view name already 
exists
 2018-10-17 19:47:40 +02:00
Celine Mercier 4802e32f72 Cython: Sequence objects: repr() method now returns a Fasta or Fastq 
formatted string
 2018-10-17 16:53:42 +02:00
Celine Mercier b027762059 Cython: export: fixed exception raising when no quality data when 
exporting to fastq
 2018-10-17 16:52:51 +02:00
Celine Mercier da0e3d4043 Cython: added full handling of NA strings when importing files 2018-10-17 16:41:15 +02:00
Celine Mercier da76f911db Cython: Views: improved repr() method 2018-10-17 15:54:03 +02:00
Celine Mercier 61ad2deeca obi uniq: Added line breaks when printing informations to cut progress 
bar properly
 2018-10-17 15:53:28 +02:00
Celine Mercier eb6d5581bd Cython: Progress bar: added a cut option to choose whether to do line 
breaks every tenth of the full bar, set to False by default for lighter
printing
 2018-10-17 15:52:26 +02:00
Celine Mercier 343dbc7e4d Cython: made the logger lighter (now prints just module name instead of 
full module path)
 2018-10-17 15:49:55 +02:00
Celine Mercier 6d018a2d28 Cython: Added 'modulename' in the config informations 2018-10-17 15:47:44 +02:00
Celine Mercier 2c2df4e098 C: Added a trick to suppress compilation warnings about an unused 
function actually called in a macro
 2018-10-17 13:13:23 +02:00
Celine Mercier 8ce6dd6d1a Updated prototypes with no arguments with a void argument as suggested 
by compilation warnings
 2018-10-17 12:00:40 +02:00
Celine Mercier df70086384 New command: obi export 2018-10-17 11:27:50 +02:00
Celine Mercier 32d8396ee2 Cython: Added fasta and fastq writers 2018-10-17 11:27:15 +02:00
Celine Mercier 6a8670d24a Cython: minor fixes 2018-10-17 11:26:13 +02:00
Celine Mercier ec73fa840a Cython: obi stats fixed to work with reworked options (forgotten in a 
previous commit)
 2018-10-17 11:25:53 +02:00
Celine Mercier 11032ec90b Cython: Sequence objects: Quality strings are now returned as bytes 
instead of str
 2018-10-17 11:24:44 +02:00
Celine Mercier 8a9ba8b0a8 Cython: Added Column line methods to get a Column line as a str or 
bytes, and elements (keys, values) with None values are not returned
anymore
 2018-10-17 11:23:07 +02:00
Celine Mercier 135d3b6e67 Cython: updated the URI decoding to handle outputs other than DMS 2018-10-17 11:21:29 +02:00
Celine Mercier 58589e04be Cython: rearranged input and output format options to have both and 
updated commands accordingly
 2018-10-17 11:19:48 +02:00
Celine Mercier e6bbe13d81 Cython: fasta and fastq parsers now return bytes and take NA string 
argument
 2018-10-17 11:16:20 +02:00
Celine Mercier 61b00d6013 Cython: fastq formatter 2018-10-09 16:41:14 +02:00
Celine Mercier 8029493c10 Cython: fasta and fastq header formatter 2018-10-09 16:41:00 +02:00
Celine Mercier aa5ee53478 Cython: fasta writer 2018-10-09 16:40:30 +02:00
Celine Mercier e31c8ea57a New command: obi history to print DMS or view history in bash, dot or 
ascii formats
 2018-10-07 19:11:36 +02:00
Celine Mercier 9e700ddc21 obi test: updated to test comments 2018-10-07 19:10:46 +02:00
Celine Mercier e9a41c5b97 Commands: updated for JSON formatted comments with history 2018-10-07 19:10:34 +02:00
Celine Mercier 35cf2962cc Cython: DMS: JSON formatted comments and history handling 2018-10-07 19:06:59 +02:00
Celine Mercier 74be3c39f0 Cython: Views: JSON formatted comments and history handling 2018-10-07 19:06:23 +02:00
Celine Mercier c6ee0bade9 Cython: Columns: goes with handling of JSON formatted comments 2018-10-07 19:04:50 +02:00
Celine Mercier ffd5bc76bf Cython utils: functions convert to bytes or str and to remove all empty 
objects from a complex object
 2018-10-07 19:03:38 +02:00
Celine Mercier 704d9b0474 Cython: Columns: added support for JSON formatted comments 2018-10-07 18:59:43 +02:00
Celine Mercier 86bb582a17 Views: implemented handling of JSON formatted comments 2018-10-07 18:56:46 +02:00