3cfe3a9b00
Improved progress display when importing files in a DMS
2019-08-29 10:12:06 +02:00
728af51cb2
Python: better display of tuple values in fasta format
2019-08-28 15:55:36 +02:00
99a397b842
obi uniq: various improvements and fixes #66
2019-08-27 20:27:36 +02:00
580db2f710
minor comment
2019-08-27 20:25:54 +02:00
dbe09f83a2
Increased the threshold of elements per line in a column before they are
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stored as a character string
2019-08-27 20:25:14 +02:00
3d1b2e8ed9
Better handling of column lines with all values at NA
2019-08-27 20:20:26 +02:00
66441e0aef
Fixed a bug when sending a DMS path to a C function from Cython
2019-08-18 19:43:51 +02:00
13952358b3
Fixed a bug where some commands wouldn't work if the input DMS was not
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in the current directory
2019-07-25 11:59:19 +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
d99702f56f
ngsfilter and alignpairedend: paired-end reads are now correctly
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reversed and labeled to be aligned correctly by alignpairedend
2019-07-23 18:56:51 +02:00
f765c6f41e
obi alignpairedend: fixed a bug where first seq was kept in result view
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instead of consensus seq
2019-07-06 16:29:32 +02:00
a83bf43ab9
obi stats: result display is now sorted
2019-07-06 16:27:51 +02:00
3d9f0352ff
obiclean parallelized
2019-06-20 19:44:04 +02:00
a04588da31
openmp on j loop (i loop probably better)
2019-05-24 16:51:04 +02:00
ac47bdce5d
history: fixed DMS history when multiple inputs
2019-03-31 15:44:20 +02:00
80068a3c19
ngsfilter: fixed parsing error
2019-03-31 15:42:30 +02:00
a3e6b7d913
obi import: fixed import of View_NUC_SEQS to another DMS
2019-03-31 15:42:07 +02:00
416c2d7ba0
Cython: made fasta formatter cleaner
2019-03-31 15:41:32 +02:00
2b8c066f8e
Cython: added possibility to output in tabular format
2019-03-31 15:39:38 +02:00
e39c1a7fbf
Cython: added tab formatter and parser (for obi export)
2019-03-31 15:38:34 +02:00
6841d879aa
obi history: fixed a bug when displaying ascii history
2019-03-31 10:51:52 +02:00
601a2cfd7d
obi uniq: various fixes...
2019-03-30 20:34:53 +01:00
f16bbca8e2
obi grep: fixed a bug where -p option didn't work
2019-03-30 19:10:42 +01:00
173483448a
Merge commit '3d842ff7'
2019-03-30 15:29:52 +01:00
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
3445579251
remove all the no more needed .cfiles
2019-03-29 16:56:58 +01:00
5007b02cbc
cleaning stage 2
2019-03-29 16:46:17 +01:00
cdd5975e8b
Cleaning first stage
2019-03-29 16:40:36 +01:00
0c466046f4
Merge branch 'pip-standard-orig-python' into 'master'
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The new install version based on classical setup.py
See merge request obitools/obitools3!1
2019-03-29 16:25:01 +01:00
bf62960ee8
Add some .ignore files
2019-03-29 15:52:54 +01:00
9c41b1e9da
Move and rename the obi.py script
2019-03-29 15:45:38 +01:00
6c52966033
Switch back to the original python source from the paster branch
2019-03-29 15:24:31 +01:00
6b9da38087
patch some relative imports
2019-03-29 15:19:44 +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
7c2787b6b3
trying to fix cython difficulties
2019-03-26 16:19:55 +01:00
14eca43eac
Import taxo
2019-03-26 16:17:44 +01:00
0b4ea49539
Convert relative import an delete cfiles
2019-03-26 16:14:03 +01:00
cd88c37a7e
Merge branch 'pip-standard' of git@git.metabarcoding.org:obitools/obitools3.git into pip-standard
2019-03-26 15:54:49 +01:00
1095a617a3
Patch relative import to absolute
2019-03-26 15:54:33 +01:00
5a05258fcb
fixed relative cython imports to be absolute
2019-03-26 15:52:59 +01:00
10ab557259
First version of the simplified setup.py script
2019-03-26 15:40:31 +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
