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b1b6833003
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2009-10-16 20:30:56 +00:00 |
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d1e473214e
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New version of setup.py script taking into account pyrex file and corresponding c file generation in the source directory
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2009-10-16 15:19:09 +00:00 |
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ef46d42467
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2009-10-16 15:18:12 +00:00 |
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0f06dda68f
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change in the script map
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2009-10-14 16:32:59 +00:00 |
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c99f4cf1e0
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change input file format from fna fasta file to standard obi fasta file. Use convert2fasta script before using fasta454filter script to convert fna file to obi file
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2009-10-14 15:28:55 +00:00 |
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d84d6d48e9
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code cleaning on obitools.word
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2009-10-14 15:05:49 +00:00 |
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ecef476a09
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2009-10-14 13:48:12 +00:00 |
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110ae8ddd8
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add a new script buildOBITaxonomy to compile a taxonomy db in obitool format from NCBI taxdump directory
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2009-10-13 14:11:45 +00:00 |
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272cfd1903
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2009-10-13 14:03:33 +00:00 |
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5aab98c74e
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Set a faster implementation of getTaxonAtRank
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2009-10-13 14:00:59 +00:00 |
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84fa97b865
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patch a bug in __contains__ method
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2009-10-13 13:53:23 +00:00 |
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73d9cdb3ed
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Add capacity to annotate sequence with taxonomy data
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2009-10-13 13:47:19 +00:00 |
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02a2cb8808
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Add capacity to annotate sequence with taxonomy data
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2009-10-13 13:44:52 +00:00 |
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5cc39dcb0e
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remove automatic annotation with taxonomy information when requested rank filter is activated
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2009-10-13 13:24:25 +00:00 |
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45b90c7f81
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remove input format option from fasta grep, use instead the new convert2fasta script
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2009-10-13 13:21:29 +00:00 |
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eb5d1a07af
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Remove fastacns2obi script and replace it by a more general one convert2fasta.py
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2009-10-13 13:14:47 +00:00 |
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678c2b3459
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Add code to automagically manage taxid attribute in sequence
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2009-10-13 12:44:32 +00:00 |
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989be1189d
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patch findTaxonByTaxid method to take care of deleted taxa
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2009-10-13 12:16:23 +00:00 |
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3acc0abb1f
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Take care of sequences with taxid < 0
Consider that these sequences have no taxid
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2009-10-12 16:56:01 +00:00 |
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e0605ce84e
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Take care of sequences with taxid < 0
Consider that these sequences have no taxid
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2009-10-12 16:54:42 +00:00 |
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2e8871fa9d
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Take care of sequences with taxid < 0
Consider that these sequences have no taxid
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2009-10-12 16:52:08 +00:00 |
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c61e0337b0
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2009-10-12 16:25:12 +00:00 |
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3ebc960bbf
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revert to old version
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2009-10-12 16:19:03 +00:00 |
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682f8d5d3e
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add annotation about rank during rank filtering
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2009-10-12 16:17:15 +00:00 |
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92c65760f7
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2009-10-12 16:15:06 +00:00 |
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011008bfa7
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add annotation about rank during rank filtering
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2009-10-12 16:04:27 +00:00 |
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e38ad9d735
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add annotation about rank during rank filtering
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2009-10-12 15:56:49 +00:00 |
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3a1d1078af
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add annotation about rank during rank filtering
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2009-10-12 15:56:30 +00:00 |
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29fcf11ece
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add annotation about rank during rank filtering
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2009-10-12 15:49:35 +00:00 |
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550627095f
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add annotation about rank during rank filtering
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2009-10-12 15:47:51 +00:00 |
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295ca9b8f6
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add option to specify input format in fastaGrep
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2009-10-12 15:34:07 +00:00 |
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1dbcc956ab
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add option to specify input format in fastaGrep
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2009-10-12 15:29:15 +00:00 |
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dac24b79f8
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add option to specify input format in fastaGrep
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2009-10-12 15:28:26 +00:00 |
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067c5cdf74
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add option to specify input format in fastaGrep
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2009-10-12 15:25:26 +00:00 |
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4c78587274
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Rename cns format to fnaFasta format
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2009-10-12 14:51:22 +00:00 |
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a05238c575
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Rename cns format to fnaFasta format
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2009-10-12 14:48:53 +00:00 |
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4b6d0b0abd
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Rename cns format to fnaFasta format
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2009-10-12 14:46:40 +00:00 |
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6f469c5d66
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path the _isNuc method to take into account sequence of length null
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2009-10-07 19:47:13 +00:00 |
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dc9867b675
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add new obitools script to convert cns fasta files to obi fasta files (add ; to headers)
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2009-09-18 17:09:34 +00:00 |
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f304309fdd
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Patch fasta reader to accelerate fasta header parsing
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2009-09-18 17:07:06 +00:00 |
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22270b2602
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Patch the rawiteritems function from WrappedBioSequence
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2009-09-18 17:06:14 +00:00 |
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5c9e608ccd
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New obitools script to analyze cDNA 454 sequences
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2009-09-18 17:05:05 +00:00 |
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9fcdb31d65
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changed name of saved rawfiles to remove the gz extension
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2009-09-18 14:24:42 +00:00 |
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657bf134e8
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patch a bug in taxonomy filter
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2009-09-18 13:57:24 +00:00 |
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b0f90494bf
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Add option to save a copy of the embl file
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2009-09-18 13:22:34 +00:00 |
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d02ca76c66
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2009-07-27 22:39:07 +00:00 |
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79dbbb8a6b
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Add new version of function fastaUniq taking into account the merge attribute
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2009-07-27 22:38:23 +00:00 |
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7219a11d3d
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patch syntax bug
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2009-07-27 17:51:52 +00:00 |
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1568bec537
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Add new script fasta2tab
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2009-07-27 17:49:26 +00:00 |
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d2a97eeb7e
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patch syntax bug
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2009-07-27 17:37:57 +00:00 |
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