obitools/ecopcr
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23 Commits 2 Branches 6 Tags
f7e25b2082ebc83fa07c8f2d2d201c3248c54d5a
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Author SHA1 Message Date
Eric Coissac
f7e25b2082 New version 0.2 of ecoPCR, with Tm computation. 
Take care file format have change. You must use corresponding version of ecogrep
You can use -t option to go back to the old format without tm computation

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@238 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2010-01-22 09:16:53 +00:00
Eric Coissac
ad6f493d0f Accept to deal with sequence in lower case 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@217 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2009-05-13 13:21:10 +00:00
Eric Coissac
1428cd7499 patch online help in ecoPCR software 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@168 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2008-05-16 08:53:11 +00:00
Eric Coissac
708b7c387e Sequence circularity, bug correction 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@167 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2008-04-28 16:46:18 +00:00
Eric Coissac
d863b7e48e Manage sequence circularity 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@166 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2008-04-28 15:49:12 +00:00
Eric Coissac
4b74056af8 change reference column for taxonomy filtering in ecogrep.c 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@165 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2008-03-12 21:26:08 +00:00
Eric Coissac
f68f4af244 Add option to ecoPCRFormat to deal with an obischema db as taxonomy source 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@158 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2008-02-08 10:27:42 +00:00
Eric Coissac
a1141a77b5 -- 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@119 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2007-09-24 10:10:03 +00:00
Eric Coissac
6835206344 Add version file 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@118 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2007-09-24 10:07:39 +00:00
Eric Coissac
45c85a9f32 git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@117 60f365c0-8329-0410-b2a4-ec073aeeaa1d 2007-09-24 10:06:00 +00:00
Eric Coissac
471bf72bf9 Add rule for ecogrep build in makefile 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@116 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2007-09-24 09:58:48 +00:00
Eric Coissac
22ecb4b842 git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@115 60f365c0-8329-0410-b2a4-ec073aeeaa1d 2007-09-24 09:48:19 +00:00
Eric Coissac
bc4c7656c6 git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@114 60f365c0-8329-0410-b2a4-ec073aeeaa1d 2007-09-24 09:48:08 +00:00
Eric Coissac
6cd1141130 Add capacity to format fasta files, with taxonomical data described in title line in the following format : 
[taxon: ####] where #### is a taxid from NCBI taxonomy. It can be as precise as possible (species, genus or even root)
		

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@13 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2007-05-02 10:10:27 +00:00
Eric Coissac
420cdb877b add a -k option to the ecoPCR binary to substitute superkingdom column by a kingdom column 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@12 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2007-03-27 16:33:50 +00:00
Eric Coissac
8c91d3d8f3 add a -k option to the ecoPCR binary to substitute superkingdom column by a kingdom column 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@11 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2007-03-27 16:29:20 +00:00
Eric Coissac
b2c307e611 replace bracket by braces 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@10 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2007-03-15 11:53:50 +00:00
Eric Coissac
9726434b46 Add patch in to eliminate sequence without taxonomic data 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@9 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2007-03-14 16:13:23 +00:00
Eric Coissac
78205cb1a3 patch to correct bug in switch between parts of the sequence database 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@8 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2007-02-15 17:23:39 +00:00
Eric Coissac
f31a7679c6 git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@7 60f365c0-8329-0410-b2a4-ec073aeeaa1d 2007-02-15 15:17:47 +00:00
Eric Coissac
8d9e519b52 Add of CECILL Licence 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@6 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2007-02-15 14:21:28 +00:00
Eric Coissac
ebe8c0b516 Initial version of ecoPCR 
git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@5 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2007-02-15 13:33:32 +00:00
Eric Coissac
f3d2273d8d git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@3 60f365c0-8329-0410-b2a4-ec073aeeaa1d 2007-02-15 13:25:04 +00:00