b24be84b0a
Add a first group of options
2017-07-25 11:14:30 +02:00
ced9a268a1
obi import: added an option to specify the NA value in the input file
...
(default is 'NA', same as in R's read.table function)
2017-07-11 12:10:33 +02:00
b729b8928f
obi less: fixed bug when the length of a view would be less than the
...
default number of lines printed
2017-07-10 17:04:02 +02:00
b6b95f26b6
obi import: Skipping sequences is now done through the iterators so that
...
sequences are not uselessly parsed
2017-07-10 17:02:30 +02:00
740d021276
obi import: fixed bugs when rewriting a column: a bug with new elements
...
names ignoring previous elements names found, a bug with the global
obi_errno being reset too late, and a bug with the column dictionary
used by obi import not being updated after rewriting a column
2017-07-07 15:33:43 +02:00
906343187b
Fixed bug with view option in obi less and obi check
2017-07-06 16:42:27 +02:00
c3cd57a9e3
Removed deprecated file
2017-07-06 10:57:14 +02:00
101f764cce
New obi import with rewriting of columns when column type or line
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elements (keys) change
2017-07-05 17:15:23 +02:00
3f5fef10b9
obi test: minor changes
2017-07-05 14:37:27 +02:00
20c72af697
Basic obi check command to check DMS and view informations
2017-07-05 13:54:19 +02:00
d252131950
Basic obi less command
2017-07-05 13:44:12 +02:00
ca16ce0bb0
Basic obi grep with new Cython API
2017-07-05 11:58:10 +02:00
4b037ae236
Updated obi test to test NUC_SEQS views and the taxonomy API
2017-04-21 12:09:04 +02:00
b998373be5
Cython API: updated the test command for the new API and deactivated the
...
other commands for now
2017-04-14 16:21:33 +02:00
381194194c
Cython API: compiling but not working
2017-03-06 16:07:02 +01:00
431c1c8c6a
Merge branch 'Eric_new_Python_API' of
...
git@git.metabarcoding.org:obitools/obitools3.git into
Eric_new_Python_API
Conflicts:
python/obitools3/obidms/_obidms.pxd
python/obitools3/obidms/_obidms.pyx
python/obitools3/obidms/_obidmscolumn_bool.pyx
python/obitools3/obidms/_obidmscolumn_str.pyx
python/obitools3/obidms/_obiseq.pxd
python/obitools3/obidms/_obiseq.pyx
python/obitools3/obidms/_obitaxo.pxd
python/obitools3/obidms/_obitaxo.pyx
python/obitools3/obidms/_obiview.pxd
python/obitools3/obidms/_obiview.pyx
python/obitools3/obidms/_obiview_nuc_seq.pxd
python/obitools3/obidms/_obiview_nuc_seq.pyx
python/obitools3/obidms/_obiview_nuc_seq_qual.pxd
python/obitools3/obidms/_obiview_nuc_seq_qual.pyx
python/obitools3/obidms/capi/obialign.pxd
python/obitools3/obidms/capi/obidmscolumn.pxd
python/obitools3/obidms/capi/obitaxonomy.pxd
python/obitools3/obidms/capi/obiview.pxd
2017-02-20 14:55:36 +01:00
f23315e26f
New Cython API: compile but doesn't work
2017-02-17 15:14:06 +01:00
e50da64ea1
The elements names when a column contains several elements per line are
...
now formatted with '\0' as separator and handled in a more optimized way
2017-01-31 16:48:06 +01:00
5c50e5b378
Embryo of code for openMP parallelization of LCS alignment but
...
deactivated for now because can't make it compile with cython/clang
2016-12-20 11:46:58 +01:00
857a5198e4
Updated `obi lcs` for the LCS alignment of two columns
2016-12-16 19:40:36 +01:00
191c83aafc
Added missing *.cfiles
2016-12-15 15:28:34 +01:00
8afb1644e9
Alignment: API rework. 'obi align' is now 'obi lcs', and the results are
...
now written to columns automatically created in the output view, all
optimally handled at the C level.
2016-12-12 11:58:59 +01:00
fa4e4ffaff
Changed the cython API to create new views so as to have different
...
functions for the different cases
2016-12-07 14:17:57 +01:00
70c49e214a
Added the kmer filter to LCS alignments, and now obiblobs containing
...
encoded sequences are directly put in int16_t arrays for the alignment
2016-11-18 16:29:28 +01:00
359578814b
Added view type property to OBIView cython class and updated obi export
...
to use it
2016-11-08 17:49:59 +01:00
51b23915ca
Added properties for Nuc_Seq cython classes (and updated commands using
...
them)
2016-11-08 16:59:32 +01:00
8291693309
obi grep: updated to work with the new line selection class and within
...
the local sequence environment, and progress bar functioning
2016-11-08 11:19:12 +01:00
4bc19c3e49
obi export: view type is now checked and progress bar functioning
2016-11-08 11:17:20 +01:00
9cd57deca9
Added OBIView_line_selection class to make new line selections
...
associated with the view to clone, and improved and renamed method
closing a view
2016-09-30 17:48:53 +02:00
d88811ed7d
Added a seed option to the obi test command for reproducible tests
2016-09-29 17:34:48 +02:00
b717e8bb8b
Added properties for the OBIView class and cleaned up deprecated code
2016-09-28 14:26:23 +02:00
03a2c8ef7c
Finished restructuring the OBIDMS_column class properties
2016-09-27 14:16:30 +02:00
a4b8349274
Added data_type property to OBIDMS_column class
2016-09-26 17:12:20 +02:00
a0bc45cc92
Added elements_names property to OBIDMS_column class
2016-09-26 16:53:16 +02:00
76f89717fe
Added alias property to OBIDMS_column cython class
2016-09-26 16:12:48 +02:00
b408a4f6eb
Changed file name limits to adapt to system limits + minor changes
2016-09-22 18:05:07 +02:00
9ac522fde1
Better obi test command
2016-09-21 17:06:35 +02:00
8f49553d5a
First version of the obi test command, testing that the OBITools3 work
...
correctly
2016-09-15 12:26:07 +02:00
8d360b0fac
Minor improvements to obi export command
2016-08-19 17:49:22 +02:00
b34769b27c
Minor improvements to obi export command
2016-08-19 17:46:55 +02:00
2d0a714e37
Basic obi export command exporting from view to fasta or fastq format,
...
for testing purposes
2016-08-19 17:40:58 +02:00
e4129610cf
Quality columns are now optional in NUC_SEQS views + minor fixes
2016-08-16 15:17:26 +02:00
cf839522e7
Minor update and fix to obi grep command
2016-08-12 17:45:44 +02:00
ad8e10f2d1
Reworked a bit alignment API
2016-08-12 15:56:07 +02:00
64a745ce0b
First very basic version of obi grep command
2016-08-11 17:32:08 +02:00
2aaa87edcc
1st version of obi align command and reworked functions that handle
...
column alignment
2016-08-10 14:51:02 +02:00
3b59043ea8
Major update: New column type to store sequence qualities. Closes #41
2016-05-20 16:45:22 +02:00
d159b921eb
Fixed obi import trying to print all lines at the end (source of
...
segfault?)
2016-04-27 13:14:19 +02:00
a6c8d35491
import command a bit modified for tests
2016-04-26 14:29:54 +02:00
7a88ca619a
First obi import (doesn't import tags yet because NA values aren't
...
handled)
2016-04-15 17:00:08 +02:00
