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
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
a9ba7744cf
obidistutils: added fPIC flag needed for linux compilation and set
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minimum python version to 3.7
2019-03-12 14:20:59 +01:00
185a95e667
cleaner Makefile
2019-03-11 15:20:10 +01:00
8835a1a983
removed -R compilaiton flag that gcc doesn't like
2019-03-07 15:55:46 +01:00
1ee50b7222
Fixed a bug when creating a column and checking the comments string if
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it was NULL
2019-03-07 15:09:59 +01:00
720bb65b24
Installation: basic Makefile that creates the shared obi3 library used
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by Cython
2019-03-07 14:01:37 +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
306da846e3
obidistutils: link obi3 C shared library instead of compiling all C
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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
af57e532da
obidistutils: create doc/sphinx dir if needed
2019-03-07 13:47:23 +01:00
52de6f2717
Update distutils for openmp and new version of pip
2019-02-19 17:30:53 +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
3015310535
Fixed a bug in kmer similarity computation where the fact that sequences
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could be switched was not accounted for
2019-02-10 21:02:24 +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
6ca6d27ecb
ecoPCR: fixed amplicon length computation bug
2019-02-06 18:11:20 +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
59017c0d6b
C: taxonomy: fixed a bug when checking for root node
2019-01-21 17:23:25 +01:00
9f6bba183f
C: Added a function to get a nucleotide at a specific index in an
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encoded sequence
2019-01-21 17:18:02 +01:00
