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elserj [Tue, 21 Sep 2010 21:10:52 +0000 (21:10 +0000)]
Modified to take input and output files as arguments (better for scripting)
svn path=/; revision=41
elserj [Tue, 21 Sep 2010 20:38:59 +0000 (20:38 +0000)]
Use subroutine to get species array and cleaned up unused code
svn path=/; revision=40
elserj [Tue, 21 Sep 2010 20:15:03 +0000 (20:15 +0000)]
Added subroutine to output all species in an array (useful for superclusters.pl, probably others)
svn path=/; revision=39
elserj [Fri, 17 Sep 2010 23:09:55 +0000 (23:09 +0000)]
Fixed Human, Mouse, and Sacc_cerevisiae gene id detection
svn path=/; revision=38
elserj [Fri, 17 Sep 2010 23:09:10 +0000 (23:09 +0000)]
Fixes the gene headers in the fasta files so that they are correctly parsed by blast. Changes it so the only info in the header is the protein/gene id.
svn path=/; revision=37
elserj [Thu, 16 Sep 2010 23:37:28 +0000 (23:37 +0000)]
took out print line in cucumber
svn path=/; revision=36
elserj [Thu, 16 Sep 2010 22:01:52 +0000 (22:01 +0000)]
Added --new option for creating a new version of the database
svn path=/; revision=35
preecej [Tue, 14 Sep 2010 22:00:26 +0000 (22:00 +0000)]
Backup Location for Mac web contents under /data/www
svn path=/; revision=34
elserj [Wed, 8 Sep 2010 21:04:22 +0000 (21:04 +0000)]
Changed the split for C.elegans since the tab in the original fasta file messes up formatdb
svn path=/; revision=33
elserj [Wed, 8 Sep 2010 00:05:37 +0000 (00:05 +0000)]
Added script to loop through and test fasta files via fasta_verify.pl
svn path=/; revision=32
elserj [Tue, 7 Sep 2010 22:25:14 +0000 (22:25 +0000)]
Script no longer needed since we don't use CSHL cvs anymore
svn path=/; revision=31
elserj [Tue, 7 Sep 2010 22:22:07 +0000 (22:22 +0000)]
Added script to find interactions given a list of genes
svn path=/; revision=30
elserj [Tue, 7 Sep 2010 22:18:52 +0000 (22:18 +0000)]
Script to test and verify fasta files are ready for InParanoid
svn path=/; revision=29
elserj [Fri, 3 Sep 2010 21:58:45 +0000 (21:58 +0000)]
Fixed find_genes subroutine for new versions of the sequence files
svn path=/; revision=28
elserj [Fri, 3 Sep 2010 21:51:48 +0000 (21:51 +0000)]
Fixed typo in final output
svn path=/; revision=27
elserj [Fri, 3 Sep 2010 21:50:06 +0000 (21:50 +0000)]
Added test for genes from find_species.pl subroutines
svn path=/; revision=26
elserj [Fri, 3 Sep 2010 00:26:16 +0000 (00:26 +0000)]
Fixed scripts for Mamathas needs, and added better use of vars
svn path=/; revision=25
elserj [Fri, 3 Sep 2010 00:24:22 +0000 (00:24 +0000)]
Updated the species detection for new species, still need to do gene headers
svn path=/; revision=24
elserj [Fri, 3 Sep 2010 00:23:46 +0000 (00:23 +0000)]
Added a test script for find_species.pl subroutines
svn path=/; revision=23
elserj [Fri, 3 Sep 2010 00:02:12 +0000 (00:02 +0000)]
Fix to skip all isomers, even if higher than .29
svn path=/; revision=22
preecej [Sun, 29 Aug 2010 06:52:57 +0000 (06:52 +0000)]
# new dir for perl web service and db broker for phenote
svn path=/; revision=21
preecej [Wed, 25 Aug 2010 23:19:48 +0000 (23:19 +0000)]
changed the string to test the version capabilities
svn path=/; revision=20
elserj [Wed, 25 Aug 2010 23:06:32 +0000 (23:06 +0000)]
Added a test file for people to use to test commit rights
svn path=/; revision=19
preecej [Wed, 25 Aug 2010 23:04:04 +0000 (23:04 +0000)]
added my personal working directory
svn path=/; revision=18
elserj [Wed, 2 Jun 2010 20:39:48 +0000 (20:39 +0000)]
Updated scripts
svn path=/; revision=17
elserj [Wed, 14 Apr 2010 21:19:14 +0000 (21:19 +0000)]
Split find_ortho scripts to do it from the super_clust table instead of inparanoid
svn path=/; revision=16
elserj [Wed, 14 Apr 2010 20:20:04 +0000 (20:20 +0000)]
Program to query inparanoid database and retrieve orthologs and paralogs
svn path=/; revision=15
elserj [Mon, 5 Apr 2010 20:12:23 +0000 (20:12 +0000)]
Updated version of supercluster to do majority voting
svn path=/; revision=14
elserj [Mon, 5 Apr 2010 20:09:48 +0000 (20:09 +0000)]
added the script that has the find_species and find_gene subroutines
svn path=/; revision=13
elserj [Wed, 25 Nov 2009 19:42:53 +0000 (19:42 +0000)]
Added module to interactively connect to database on floret
svn path=/; revision=12
elserj [Fri, 6 Nov 2009 18:36:24 +0000 (18:36 +0000)]
updated versions of flowering_interaction and inparanoid_output_parse, added supercluster and inparanoid_orthologs scripts
svn path=/; revision=11
elserj [Wed, 30 Sep 2009 20:36:17 +0000 (20:36 +0000)]
Added subroutine to only add the gene or locus id to db instead of entire gene header. Still might not be right for some species.
svn path=/; revision=10
elserj [Tue, 22 Sep 2009 20:04:59 +0000 (20:04 +0000)]
Fixed the species identification
svn path=/; revision=9
elserj [Tue, 22 Sep 2009 19:41:47 +0000 (19:41 +0000)]
Fixed the file so it wasn't a symlink
svn path=/; revision=8
elserj [Tue, 22 Sep 2009 19:41:25 +0000 (19:41 +0000)]
svn path=/; revision=7
elserj [Tue, 22 Sep 2009 19:36:12 +0000 (19:36 +0000)]
script to populate the SQL database with data from inparanoid
svn path=/; revision=6
elserj [Mon, 31 Aug 2009 21:45:57 +0000 (21:45 +0000)]
Added scripts for running inparanoid and copying the cvs repo from cshl to OSU
svn path=/; revision=5
elserj [Fri, 14 Aug 2009 22:43:48 +0000 (22:43 +0000)]
testing
svn path=/; revision=4
testuser [Fri, 14 Aug 2009 21:28:07 +0000 (21:28 +0000)]
made test change
svn path=/; revision=3
elserj [Fri, 14 Aug 2009 21:26:43 +0000 (21:26 +0000)]
Added version to tree script
svn path=/; revision=2
elserj [Fri, 14 Aug 2009 21:18:55 +0000 (21:18 +0000)]
Justin's initial import of his scripts
svn path=/; revision=1
projects / old-jaiswallab-svn / .git / log