ffe2485e94
Genbank parser: now reading ORIGIN lines with comments without
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triggering error
2020-05-28 20:41:34 +02:00
f13f8f6165
obi import: minor doc/display improvements
2020-05-20 11:46:29 +02:00
ca6e3e7aad
obi import: fixed to work with seq genbank extension
2020-05-20 10:28:14 +02:00
a72fea3cc9
Python: fasta parser: fixed a bug stopping the program when the last
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line contained a single nucleotide
2020-05-12 11:24:12 +02:00
cd9cea8c97
obi import: fixed critical bug where the last entry of embl and genbank
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files was not imported
2020-04-09 19:26:27 +02:00
b1f3e082f9
ngsfilter: fixed a bug when there is only one tag introduced in latest
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edit
2020-01-06 13:53:38 +01:00
53f18316b0
ngsfilter: made more robust and practical to use with empty tags
2019-11-29 15:21:08 +01:00
3cfe3a9b00
Improved progress display when importing files in a DMS
2019-08-29 10:12:06 +02:00
9752ff8494
embl parser: information display about progress when parsing multiple
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files
2019-07-23 18:59:07 +02:00
80068a3c19
ngsfilter: fixed parsing error
2019-03-31 15:42:30 +02:00
173483448a
Merge commit '3d842ff7'
2019-03-30 15:29:52 +01:00
c293cfabbb
Python: embl parser: fixed a bug preventing taxids from being parsed
2019-03-30 15:15:49 +01:00
3445579251
remove all the no more needed .cfiles
2019-03-29 16:56:58 +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
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
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
478d19ab43
Cleaner stderr prints
2019-03-13 18:36:31 +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
29c56572cf
Add cfiles everywhere ;-)
2019-02-19 15:04:30 +01:00
4ddd1a1c37
embl iterator: only option on embl directories now works as intended
2019-02-12 16:46:08 +01:00
e18b762d81
Weird buggy Eclipse commit with nothing changed
2018-10-21 17:35:18 +02:00
da0e3d4043
Cython: added full handling of NA strings when importing files
2018-10-17 16:41:15 +02:00
6a8670d24a
Cython: minor fixes
2018-10-17 11:26:13 +02:00
303648bd47
Cython: embl file parser
2018-07-28 17:14:10 +02:00
3e8c187f0b
Cython API: added EMBL parser and files to import are now read in binary
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mode
2018-07-28 16:57:01 +02:00
6825fc13ab
Cython API: added ngsfilter file parser
2018-03-21 16:41:25 +01:00
49c17ab7b4
Cython API: added tabular file parser
2018-03-21 16:41:09 +01:00
15e43bb9a1
Cython API: obi import can now import ngsfilter files and tabular files
2018-03-12 18:10:43 +01:00
74d880b817
Fixed default quality offset
2018-02-12 14:43:44 +01:00
d21f4a6f90
Header parser: identifiers ending with ';' are now handled
2017-11-24 17:59:52 +01:00
74f15d1a23
Cython API: Various fixes in input handlers (parsers, openers etc).
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Mostly working but not bug-free
2017-08-20 17:37:51 +02:00
b9c65a871f
Patch decoding of URL
2017-07-28 12:41:28 +02:00
89e2f80fd8
Goes with previous commit
2017-07-27 19:43:00 +02:00
7112f44fb7
Bug fixes for input handlers, openers, parsers etc. Compiling but not
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tested
2017-07-27 19:42:44 +02:00
ec65f00cf2
Complete the fasta iterator to manage new input options
2017-07-27 16:05:30 +02:00
8d9cdb4d03
Complete the fastq iterator to manage new input options
2017-07-27 16:05:17 +02:00
8781ecab1f
Add a factory checking the file format and returning the correct
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iterator. First version working only with fasta and fastq nucleic
formats
2017-07-27 16:02:52 +02:00
b6b95f26b6
obi import: Skipping sequences is now done through the iterators so that
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sequences are not uselessly parsed
2017-07-10 17:02:30 +02:00
0526386337
first working DMS class
2016-12-27 06:17:45 +01:00
8f0462c407
Merge branch 'master' into Eric_version_for_sequence
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Conflicts:
python/obitools3/obidms/_obidmscolumn_seq.pyx
2016-08-03 10:09:20 +02:00
a8ed57dc6e
few small changes
2016-05-21 12:29:55 +02:00
5a78157112
increase parsing speed of the header
2016-05-21 10:29:11 +02:00
0b9a41d952
Patch a bug about the reading of the last sequence
2016-05-21 10:28:03 +02:00
45c9c5075c
A first version of the fasta parser
2016-04-01 18:15:54 +02:00
20b97c972b
Add boolean type in the tag evaluation
2016-04-01 13:42:24 +02:00
efc4a4a3c6
Reduce the call count to eval. This reduce by 3 the time of fast(q|a)
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header processing
2016-04-01 08:54:06 +02:00
1cd35b3359
firt version of a fastq parser
2016-03-31 10:47:12 +02:00
