obitools/ecopcr
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25 Commits 2 Branches 6 Tags
1c30a8604f770937a4246cb3148de6b93b2b6aee
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Author SHA1 Message Date
Eric Coissac
1c30a8604f git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@240 60f365c0-8329-0410-b2a4-ec073aeeaa1d 2010-01-22 09:19:36 +00:00
Eric Coissac
985d067bd8 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@239 60f365c0-8329-0410-b2a4-ec073aeeaa1d
 2010-01-22 09:19:19 +00:00
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