370fb9272c
obi uniq: better typing
2018-02-12 14:38:07 +01:00
c8097e14e1
obi import: removed old traces
2018-02-12 14:36:56 +01:00
01ef85658c
New command: obi alignpairedend
2018-02-12 13:30:06 +01:00
f5a00c9322
Cython alignment library
2018-02-12 13:28:20 +01:00
156fb04e88
Implemented functions to build reverse complement sequences
2018-01-05 16:08:36 +01:00
428c4eb5e6
obi import: fixed creation of quality columns (to discuss)
2017-12-19 11:07:00 +01:00
1a5b499b5c
Cython API to add an OBI_QUAL column after creating a view
2017-12-19 11:06:24 +01:00
b7b8ba7e5a
Better handling of elements names in Cython
2017-12-13 23:12:14 +01:00
e9e7fac999
New obi uniq: stores columns with too many elements per line as
...
character strings, and keeps a minimum of things in the memory
2017-12-13 22:49:08 +01:00
1fd3323372
Columns: elements names informations are now kept in a memory arena of
...
adapted size in the header, and added a boolean in the header indicating
whether the values should be evaluated (typically character strings to
be evaluated in Python)
2017-12-13 22:46:50 +01:00
2df5932b67
Cython column API: fixed a memory leak, optimized the reading of
...
elements names, added a __len__ method to Column_line, and the API for
columns with character strings to evaluate
2017-12-13 22:27:36 +01:00
b93b982a18
Cython: added an option for input taxdump and and an option for the
...
maximum number of elements in columns with multiple elements per line
2017-12-13 22:25:15 +01:00
d21f4a6f90
Header parser: identifiers ending with ';' are now handled
2017-11-24 17:59:52 +01:00
9e3ac477eb
OBIDMS: Opened DMS now have a counter associated so that DMS are not
...
actually opened several times by the same program, which triggers the
cleaning of unfinished views and columns (to discuss)
2017-11-24 17:58:47 +01:00
ee5d647d0d
Taxonomy: fixed a bug un parental tree iterator
2017-11-24 17:55:17 +01:00
38fef5b9d4
obi test: better taxonomy testing
2017-11-24 17:54:10 +01:00
9a50803c00
Added tuple columns containing immutable indexed data arrays of any type
2017-11-15 13:48:59 +01:00
43f65e7fd0
obi uniq: fixed bug where dictionary indexes were not read properly, and
...
added view rollback in case of an exception.
2017-10-26 19:00:05 +02:00
dfd51939a0
Views are now rollbacked if an error occurs, and unfinished views and
...
columns are deleted when an OBIDMS is opened.
2017-10-26 18:58:48 +02:00
1ae634d56b
Added atexit command to obi import, obi uniq and obi less
2017-10-16 11:09:55 +02:00
04e065094a
All DMS opened by a program are now listed and closed with atexit system
2017-10-16 10:35:07 +02:00
5ddd1d9ae6
obi uniq: added taxonomy handling
2017-10-04 16:13:07 +02:00
f2ece573ff
Removed deprecated command
2017-10-04 16:09:41 +02:00
fb9b219abe
Fixed a bug with taxonomy URIs not being read correctly
2017-10-04 16:00:30 +02:00
09a5f89849
Column API: improvements to be more flexible when referring to elements
...
in columns with several elements per line.
2017-10-04 15:59:23 +02:00
535692b020
Taxonomy: new functions and improvements
2017-10-04 15:55:13 +02:00
0ab081f79e
Updated obi test to work with changes in taxonomy API
2017-10-04 15:50:32 +02:00
1cb05de7e3
Basic obi less
2017-10-04 15:46:26 +02:00
532d8e9cd7
obi import: small efficiency improvement when dealing with NA values
2017-10-04 15:44:48 +02:00
b4088a7928
Cython API: Added basic taxonomy option
2017-10-04 15:42:17 +02:00
ae24a807da
obi uniq: added the option to merge ids, except it only works on small
...
sets until lists are implemented properly using obiblobs
2017-09-25 17:28:03 +02:00
75c15594c4
obi uniq: added option to use categories additionally to the sequence to
...
determine uniqueness
2017-09-25 10:56:43 +02:00
41dec03448
Merge branch 'master' of git@git.metabarcoding.org:obitools/obitools3.git
2017-09-18 16:08:31 +02:00
a776e46e6d
Add the command name in the log
2017-09-15 14:51:13 +02:00
0e140df0fb
Cython API: added some imports in __init__ files
2017-09-14 18:30:04 +02:00
73bca6288f
New obi uniq
2017-08-20 18:04:21 +02:00
6a2759eee6
obi import with new input/ouput API
2017-08-20 17:58:36 +02:00
663a1a1091
Cython API: column elements: added possibility to check if an element
...
exists from its index, and a dict-like get() method
2017-08-20 17:44:05 +02:00
c6d5436a58
Cython API: fixed a bug where iteration on a NUC_SEQS view would not be
...
done correctly (bug appeared with optimization modifications done
lately)
2017-08-20 17:41:41 +02:00
47cad285d6
Cython API: fixed 2 little bugs in Seq API
2017-08-20 17:39:30 +02:00
74f15d1a23
Cython API: Various fixes in input handlers (parsers, openers etc).
...
Mostly working but not bug-free
2017-08-20 17:37:51 +02:00
7f1ff49aa2
Cython API to import a column and a view from a DMS to another DMS
2017-08-03 16:34:02 +02:00
407f61a408
Add the possibility to create temporary objects like a temporary
...
directory and a temporary DMS
2017-07-28 16:33:19 +02:00
35b0c55a8c
Cython API: various improvements and checks
2017-07-28 13:15:13 +02:00
b9c65a871f
Patch decoding of URL
2017-07-28 12:41:28 +02:00
84bb93096f
Cython API: fixes and improvements in Column API
2017-07-28 10:27:04 +02:00
01c69e7e25
Cython API: fixed a bug when printing a column
2017-07-28 10:01:56 +02:00
adf5cbef97
Added DMS method to create a DMS if it doesn't already exists, otherwise
...
opens it
2017-07-28 09:55:43 +02:00
da48a9d1af
Patch group of option : types must be callable not a string
2017-07-28 09:36:18 +02:00
9482c663c0
minor comments and changes
2017-07-27 19:46:34 +02:00
