173483448a
Merge commit '3d842ff7'
2019-03-30 15:29:52 +01:00
52b3a9fc39
C: taxonomy: fixed a segfault on linux when trying to fclose an unopened
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file
2019-03-30 15:19:12 +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
0847d618d6
fixed typo
2019-03-30 15:14:30 +01:00
9fcebd7643
C: build_reference_db: made some errors more explicit
2019-03-30 15:11:49 +01:00
5d842ff7e7
Clean the manifest of old files
2019-03-29 16:58:45 +01:00
3445579251
remove all the no more needed .cfiles
2019-03-29 16:56:58 +01:00
995a66b488
Add the new script emplacement
2019-03-29 16:55:23 +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
2774422224
Patch the way of installing the obi main command
2019-03-29 16:21:28 +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
3a6d1be795
remove the old distutils
2019-03-29 15:42:45 +01:00
6c52966033
Switch back to the original python source from the paster branch
2019-03-29 15:24:31 +01:00
460187970f
First version compiling the code correctly
2019-03-29 15:22:10 +01:00
52b8008bdc
Add the location of install
2019-03-29 15:21:30 +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
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
50e7cd61a6
added math.h import where needed
2019-03-13 11:17:25 +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
