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7383f8ec66
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bug correction
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2008-04-08 15:15:05 +00:00 |
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6478c6e143
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Add OBO ontology parser
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2008-04-08 15:14:47 +00:00 |
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629b0659f9
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2008-04-08 11:00:08 +00:00 |
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6605d1bdb5
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Add a new generic parser
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2008-04-03 05:51:41 +00:00 |
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de2b771e19
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Add some docs to fasta module
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2008-03-18 17:02:40 +00:00 |
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f5c818bff2
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tools for parse cns data files
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2008-03-18 15:15:46 +00:00 |
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6e5e23c1fe
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add a join function to join array
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2008-03-18 15:14:54 +00:00 |
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4fa7a3b009
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Convert fastaComplement to the new option management system
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2008-03-17 11:30:20 +00:00 |
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835b7ca574
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Convert fastaLength to the new option management system
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2008-03-17 10:40:35 +00:00 |
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3059874da2
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bug correction on parsing error
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2008-03-12 15:44:38 +00:00 |
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fa858bebf3
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add gbmode parameter to formatFasta function
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2008-03-12 15:44:04 +00:00 |
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8a1abbf1fb
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Add an extra column in ecoTag output to indicate lower identity bound used in identification process
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2008-03-12 15:43:07 +00:00 |
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7835cfaf21
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Add 'in' operator to BioSequence
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2008-03-12 14:31:08 +00:00 |
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12516c9a07
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Add management of parsing error for qualifier
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2008-03-12 14:30:30 +00:00 |
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6d7f8d1a3b
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Add a skipError parameter on the getFeatureTable method
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2008-03-12 14:29:03 +00:00 |
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7f0b6671b3
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Add a default -D (--DEBUG) option that switch logging in debug mode.
Now all scripts have this option
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2008-03-12 14:27:31 +00:00 |
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e93a2ea2ec
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Allow to define special tag regex in fasta reading functions
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2008-03-11 16:29:31 +00:00 |
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b73243df25
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Add extractCDS.py script to extract CDS from Genbank DB file.
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2008-03-10 18:29:33 +00:00 |
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ad1c211c8d
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remove call to old oligo module
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2008-03-06 16:02:13 +00:00 |
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08a709592f
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Add functionnal version of bron and carbosh algorith for clique finding
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2008-03-06 15:27:17 +00:00 |
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a92f16f253
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commit test
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2008-03-04 17:06:56 +00:00 |
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731fc73c4d
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2008-02-19 18:02:44 +00:00 |
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6584f069ed
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Add log in data fetching on stderr
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2008-02-19 18:02:06 +00:00 |
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04f2a50a1a
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2008-02-19 17:52:06 +00:00 |
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62c87a3986
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2008-02-19 17:51:23 +00:00 |
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6dd5422caa
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2008-02-19 17:21:45 +00:00 |
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fb633f8472
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2008-02-19 17:21:26 +00:00 |
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241e01b277
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New version of the API documentation
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2008-02-19 17:05:59 +00:00 |
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7ef35faac3
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Add CacheDB class to utils module
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2008-02-19 17:00:20 +00:00 |
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1c58d751d3
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patch on fastaComplement script, need to be refactored
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2008-02-19 16:59:43 +00:00 |
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60c0a54d73
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Add new script to dump sequence by blast request -- initial version not fully functional
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2008-02-19 16:58:53 +00:00 |
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2022b632f5
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add two new script for sequence statistics
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2008-02-19 16:56:36 +00:00 |
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ee8e3fa231
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patch fasta parser to deal with extra spaces in tag values
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2008-02-19 16:54:51 +00:00 |
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646f3d5f72
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code refactoring to rename oligo to word
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2008-02-19 16:53:40 +00:00 |
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0909345694
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large improvement in table management
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2008-02-19 16:52:50 +00:00 |
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93a8e4cddc
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modify complement encoder to deal with lower case sequences
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2008-02-19 16:52:15 +00:00 |
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0583a2373e
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large improvement of the genbank access and parsing
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2008-02-19 16:51:04 +00:00 |
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7d65f763e4
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obliged sequence to be in lower case
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2008-02-19 16:50:16 +00:00 |
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2e24afc639
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new module that resume input parsers and output formaters
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2008-02-19 16:49:37 +00:00 |
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d26aa7aeb7
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add lock feature to limit concurrent access in multithreaded scripts
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2008-02-19 16:48:41 +00:00 |
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f08c0876b3
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patch location and feature module
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2008-02-19 16:47:47 +00:00 |
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ecb2e48623
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Add blast interface module
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2008-02-19 16:47:20 +00:00 |
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78c36080a2
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2008-02-15 11:01:10 +00:00 |
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c020231e91
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merge genbank and genpep module
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2008-02-15 10:39:03 +00:00 |
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e5fe49ba1e
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Change id sequence definition in ecopcr2fasta script
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2008-02-13 16:06:01 +00:00 |
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c31cc3dea0
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Change id sequence definition in ecopcr2fasta script
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2008-02-13 16:04:08 +00:00 |
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f72c279496
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rename nucdb package to biodb
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2008-02-08 17:15:49 +00:00 |
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f6dc6139e3
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rename nucdb package to biodb
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2008-02-08 17:15:33 +00:00 |
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88074cfe24
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2008-02-01 09:39:36 +00:00 |
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92392ecbbd
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2008-02-01 09:35:44 +00:00 |
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