0b0445106b
added a bad iterator/parser for a specific file (for Pierre)
2012-12-20 13:39:50 +00:00
c0834dac75
[MOD] set 'mode' value to 'joined' (because join may be evaluated as a string method)
2012-12-19 14:54:33 +00:00
e5ead0c811
[MOD] changed method rawiteritems of abstract class BioSequence (the key=value tags were not parsed before printing i.e. were not visible)
2012-12-19 14:38:18 +00:00
4da37a7029
[MOD] re-added 'head' 'singleton' and 'internal' as keywords of the sequence for old scripts compatibility purpose
2012-11-23 12:58:53 +00:00
0b02d7535c
patch a bug in solexapairend
2012-11-13 20:34:46 +00:00
8177aaef3f
patch a bug
2012-11-13 16:44:34 +00:00
a4932a40a4
@tweet:Change the management of unaligned pairend reads
2012-10-26 12:56:47 +00:00
735978864c
2012-10-26 12:16:21 +00:00
fcab3899ae
2012-10-26 12:13:24 +00:00
8a41aa5eac
2012-10-26 12:12:44 +00:00
528a9dc883
2012-10-26 11:42:25 +00:00
3332032b6b
remove .c file generated by cython from the archive
2012-10-26 11:19:08 +00:00
ad043d25b5
Add local version of the counter class
2012-10-24 14:36:09 +00:00
53084c703e
patch the addEdge method
2012-10-22 21:52:39 +00:00
99afea377e
added the possibility to simulate sequencing errors in obingssim
2012-10-19 11:33:19 +00:00
29ea64ea04
fixed a little error in convertEcoPCRDB
2012-10-19 11:31:42 +00:00
923ba6a710
fixed a few old errors in the input/output format options help
2012-10-17 17:03:20 +00:00
dacaedf474
made obitaxonomy better and added a -P option to force the adding of taxa under an ancestor specified in the sequences' headers
2012-10-17 13:55:16 +00:00
3faf2c7936
updated ecoFindTaxids to read SILVA databases.
2012-10-17 13:53:16 +00:00
14bbcd66b3
fixed ecoTag's help
2012-10-17 13:52:42 +00:00
c18ce3ae1b
2012-10-16 14:17:19 +00:00
308abc5d57
updated obitaxonomy to read taxonomy paths when adding taxa from a file.
2012-10-16 12:53:39 +00:00
82f743447c
updated ecoFindTaxids to read UNITE databases.
2012-10-16 12:52:47 +00:00
4a9fbc367b
fixed a little bug
2012-10-12 12:59:42 +00:00
b7762e64c4
fixed ecoTag's help
2012-10-11 15:22:33 +00:00
0ef537aa4b
Added new options in obitaxonomy to add all the taxa from a file (-F, -S, -A)
2012-10-11 14:24:32 +00:00
4ce1df9cf1
new script ecoFindTaxids, find/add taxids identified from an ecoPCR database to a file with taxa names
2012-10-11 14:21:01 +00:00
ad9cf0653f
ADD: new option --fieldcutname to make ecoTag work with paired-end sequences (experimental)
2012-10-11 14:20:04 +00:00
4e33a4ab0d
@tweet:New bug release version
2012-10-10 08:44:25 +00:00
aa2931448a
2012-10-10 08:43:21 +00:00
43c7072515
add --run option in the tagEditOptions
2012-10-09 14:19:51 +00:00
3feea5a3e0
obiclean multi ratio
2012-10-09 12:54:21 +00:00
180abf68e4
fixed the subTreeIterator
2012-10-05 12:22:37 +00:00
d5106b0bff
deleting option double :'(
2012-10-01 15:13:58 +00:00
07ec017bd7
deleting option double :'(
2012-10-01 15:11:16 +00:00
0b45a77787
added an option "--hasancestor" to filter sequences with an ancestor of a specified taxid
2012-10-01 14:33:40 +00:00
4cbcf7c1ef
fix a little thing with convertEcoPCRDB
2012-09-21 13:32:45 +00:00
766ca3a0c6
@tweet: switch version number to 0.2.500
2012-09-19 16:35:36 +00:00
7162c53b0f
patch a division by zero error in the buildconsensus function
...
@tweet:patch a division by zero bug in the new version of solexapairend
2012-09-11 06:15:06 +00:00
1fd7d7b9f0
@tweet: Fix a memory leak in fastq readers.
2012-09-10 20:25:12 +00:00
c49f1131cd
changed a little something in convertEcoPCRDB to make it "cleaner"
2012-08-27 11:47:00 +00:00
45fb08d428
adding tool : convertEcoPCRDB. Converts an ecoPCR database to the format chosen by the user.
2012-08-27 11:38:35 +00:00
acb3b5502f
Add alignment quality check in solexapairend.
...
Upper cases in the solexapairend script name are removed to be consistent with other obitools names
a new command solexapairendnull is added to estimate null distribution of solexapairend alignement scores
@tweet: A new version of solexapairend including alignment quality check
2012-08-24 15:34:15 +00:00
ef640405a7
Add alignment quality check in solexapairend.
...
Upper cases in the solexapairend script name are removed to be consistent with other obitools names
a new command solexapairendnull is added to estimate null distribution of solexapairend alignement scores
2012-08-24 15:33:01 +00:00
a363530e4d
just a commit test
...
@tweet: a commit of ngsfilter
with less bug
2012-08-22 09:51:07 +00:00
1052c326a4
just a commit test
...
@tweet: a commit of ngsfilter
with less bug
2012-08-22 09:49:54 +00:00
7d1b75ab82
just a commit test
...
@tweet: a commit of ngsfilter
with less bug
2012-08-22 09:33:58 +00:00
aa8c2c736f
just a commit test
...
@tweet: a commit of ngsfilter
with less bug
2012-08-22 09:29:46 +00:00
baa5b51c5b
A new version of ngsfilger without a bug about error count between primers and sequence
2012-08-20 17:00:50 +00:00
0c001ae0be
A new version of ngsfilger without a bug about error count between primers and sequence
2012-08-20 16:49:31 +00:00
