ce686e9569
obi import: progress bar fixed when using --only option
2019-03-30 15:16:57 +01:00
c293cfabbb
Python: embl parser: fixed a bug preventing taxids from being parsed
2019-03-30 15:15:49 +01:00
ee9947217c
alignpairedend: fixed the worst memory leak and the handling of the case
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where 0 common kmers are found
2019-03-29 11:16:25 +01:00
ceaafca427
ngsfilter: fixed a bug (maybe 2) in the algo for the choice of the
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reverse primer when running on unaligned sequences
2019-03-29 10:56:17 +01:00
8e70bf1ee1
obi import: fixed bug when rewriting a column (keeping wrong type in
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import module)
2019-03-26 14:56:18 +01:00
d8a7bd42bd
Cython API, taxonomy: fixed parental tree iterator (skipped second to
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last taxon, in OBI1 too)
2019-03-26 14:08:54 +01:00
06178d9d61
Genbank file parser functions that should have been included in a
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previous commit
2019-03-20 11:44:43 +01:00
3abe1b7ace
obi_errno_to_exception function now properly reads obi_errno global
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variable directly
2019-03-20 11:43:12 +01:00
802a3f5933
data import: entries now counted if there are multiple files
2019-03-18 18:16:39 +01:00
7e20870719
Added genbank parser
2019-03-15 16:06:27 +01:00
e8090a44c9
Fixed the ultimate bug with embl (and genbank) parsers: raising any
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exception in a python generator makes it unable to resume. So now,
exceptions are not raised but printed, then functions return None and
that's handled at higher level.
2019-03-15 16:06:06 +01:00
832f582802
Fixed no-skip-on-error option :p
2019-03-15 16:04:04 +01:00
58d0c850c2
Made skip on error option True by default......
2019-03-15 15:50:40 +01:00
7737211ac2
Small fix in embl and genbank features parser
2019-03-15 15:50:11 +01:00
c953f0cb00
Fixed embl import where sequences were not imported as Nuc_Seq objects
2019-03-15 11:41:07 +01:00
bb045c3ae9
added TAXID_COLUMN to C API declarations for Cython
2019-03-15 11:40:06 +01:00
2a4f1b8feb
obi import: now properly uses macros for column names
2019-03-15 11:39:21 +01:00
24a63f8732
URIs: URIs built with autocomplete now work too
2019-03-15 10:52:27 +01:00
478d19ab43
Cleaner stderr prints
2019-03-13 18:36:31 +01:00
e3c565d6be
Cleaner progress bar
2019-03-13 18:36:05 +01:00
d88390c6d8
Cython API: when importing a file in a DMS, its length is computed
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beforehand for the progress bar
2019-03-13 18:35:32 +01:00
49d5f6fb1e
removed deprecated comment
2019-03-13 11:17:04 +01:00
b45c2ee653
Cython API: cleaner column rewriting API
2019-03-13 11:13:55 +01:00
6afd1294a7
Cython API: Views: fixed a bug when rewriting a column with different
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attributes (last line is not written anymore)
2019-03-12 16:40:30 +01:00
2a1ab9db29
Cython API, Views: guessing an obitype from a python value is now done
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through the corresponding functions in utils
2019-03-07 13:57:37 +01:00
4bc52c08c2
minor changes
2019-03-07 13:53:37 +01:00
29c56572cf
Add cfiles everywhere ;-)
2019-02-19 15:04:30 +01:00
de3d12af17
Renamed CAPI file
2019-02-19 14:50:30 +01:00
9ccddd5280
better cfiles
2019-02-19 14:11:29 +01:00
e026e9ec83
Fixed the new alignpaired end to work after ngsfilter with the 9879847
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possible cases
2019-02-17 18:32:35 +01:00
4ddd1a1c37
embl iterator: only option on embl directories now works as intended
2019-02-12 16:46:08 +01:00
08bcbcd357
ngsfilter: reworked to use apat library
2019-02-06 18:13:54 +01:00
04a3682307
Cython API: added API to use apat (pattern search) C library
2019-02-06 18:12:49 +01:00
8f18907566
Cython API: changed revcomp attribute of Nuc_Seq class to is_revcomp to
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be more explicit
2019-02-06 18:09:11 +01:00
0b62619e4e
Various commentaries and insignificant fixes
2019-01-21 17:32:44 +01:00
c7f5b8d980
Alignpairedend: added alignment using shifting with best kmer similarity
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(low level layer in C and Cython API)
2019-01-21 17:30:46 +01:00
2a6a112d29
obi import: fixed writing quality in views when appropriate (but still
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not a satisfying solution)
2018-12-11 19:33:55 +01:00
c437931a35
Cython: fixed history dot graph for all views, and fixed history
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recording for build_ref_db and ecotag
2018-12-10 17:09:00 +01:00
eb586b2f53
New command and C functions: obi ecotag
2018-12-09 19:19:32 +01:00
579f56bb54
obi align (pouic): fixed bug with the saved config when aligning 2
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different views
2018-12-09 19:15:58 +01:00
6acb21712a
Missing commit for build_ref_db: C API file for cython
2018-12-09 19:11:59 +01:00
6f27734d71
Cython: fxed a bug in INT tuple columns where values were converted to
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double instead of int
2018-11-27 16:14:56 +01:00
ece942e771
new command: build_ref_db to build a reference database with metadata
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for the taxonomic assignment of sequences
2018-11-27 16:11:18 +01:00
4d51f4f015
obi import: better checking of whether to import quality
2018-11-19 11:23:39 +01:00
b0da36cb48
New command: obi align, except it's called obi pouic for now because of
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a Cython compilation bug
2018-11-07 16:05:48 +01:00
d1f1fd432e
Minor fixes
2018-11-07 16:04:17 +01:00
75a28929a7
Renamed Cython alignment library in an attempt to limit some compilation
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bugs potentially involving name conflicts
2018-11-07 16:03:32 +01:00
8faabd3ebf
Cython, URI: Fixed a bug when using an output URI with just a view name
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to use the default DMS
2018-11-02 19:04:27 +01:00
35f3e7c30b
All commands now handle outputing to another DMS + small fixes
2018-11-02 19:03:09 +01:00
d09aa43133
Cython API: added a function to get the full path to the DMS directory
2018-10-31 14:46:25 +01:00
