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elserj [Wed, 6 Apr 2011 21:44:15 +0000 (21:44 +0000)]
Changed Zea mays to use the header from maizesequence.org
svn path=/; revision=90
elserj [Thu, 10 Mar 2011 22:52:55 +0000 (22:52 +0000)]
Added script that will take the list of protein coding genes and repeated genes from IPRscan and removes them from a fasta file
svn path=/; revision=89
preecej [Mon, 14 Feb 2011 22:56:30 +0000 (22:56 +0000)]
First iteration: Determine mapped ChEBI molecules listed in arabidopsis
but not in rice.
svn path=/; revision=88
preecej [Wed, 9 Feb 2011 00:04:01 +0000 (00:04 +0000)]
temp script for correcting a curatorial data problem in the AraCyc v7.0
(BioPax, lvl-2) file
-This line, and those below, will be ignored--
A perl_singletons/aracyc_to_reactome_conversion
A perl_singletons/aracyc_to_reactome_conversion/convert_bad_pub_authors_to_years.pl
svn path=/; revision=87
preecej [Mon, 7 Feb 2011 23:23:07 +0000 (23:23 +0000)]
removed rice references to make generic for other species
svn path=/; revision=86
elserj [Fri, 28 Jan 2011 23:43:56 +0000 (23:43 +0000)]
Add species
svn path=/; revision=85
elserj [Fri, 28 Jan 2011 00:47:30 +0000 (00:47 +0000)]
Add citrus, eucalyptus and apple to gene detection
svn path=/; revision=84
elserj [Sat, 8 Jan 2011 01:31:32 +0000 (01:31 +0000)]
expanded to .fa as well as .fasta files. Also, seperate name into genus+species so easier to read
svn path=/; revision=83
elserj [Sat, 8 Jan 2011 01:29:38 +0000 (01:29 +0000)]
Script to be used for detection of obsolete terms in PO, to be used as part of the pipeline when loading the DB
svn path=/; revision=82
elserj [Fri, 29 Oct 2010 22:33:22 +0000 (22:33 +0000)]
Script to find some stats about a species supercluster data
svn path=/; revision=81
preecej [Wed, 27 Oct 2010 03:30:50 +0000 (03:30 +0000)]
moved SMW extension declarations to fix autocompletion and premture value
svn path=/; revision=80
preecej [Wed, 27 Oct 2010 02:20:42 +0000 (02:20 +0000)]
added prototyping dir for backup and versioning
svn path=/; revision=79
preecej [Wed, 27 Oct 2010 02:13:40 +0000 (02:13 +0000)]
renamed www to mac_www and added folder for semantic wiki code, esp versioned php but also test scripts
svn path=/; revision=78
elserj [Fri, 22 Oct 2010 23:59:35 +0000 (23:59 +0000)]
Fix location of find_species.pl
svn path=/; revision=77
elserj [Fri, 22 Oct 2010 23:53:29 +0000 (23:53 +0000)]
Fixed gene detection in C.elegans
svn path=/; revision=76
elserj [Fri, 22 Oct 2010 23:50:06 +0000 (23:50 +0000)]
Try that again
svn path=/; revision=75
elserj [Fri, 22 Oct 2010 23:49:33 +0000 (23:49 +0000)]
Another typo
svn path=/; revision=74
elserj [Fri, 22 Oct 2010 23:48:37 +0000 (23:48 +0000)]
Fixed typos
svn path=/; revision=73
elserj [Fri, 22 Oct 2010 23:46:16 +0000 (23:46 +0000)]
Fixed location of find_species.pl check
svn path=/; revision=72
elserj [Fri, 22 Oct 2010 23:42:26 +0000 (23:42 +0000)]
Added new species for Kathryn Bushley
svn path=/; revision=71
preecej [Thu, 21 Oct 2010 01:02:59 +0000 (01:02 +0000)]
- fixed bug that ignored multiple reactome id's in RiceCyc name during mapping ouput
- added ability to map on Reactome Compound Names
- made mapping on RiceCyc Names optional
svn path=/; revision=70
preecej [Tue, 19 Oct 2010 06:42:46 +0000 (06:42 +0000)]
laptop svn connectivity test
svn path=/; revision=69
preecej [Mon, 18 Oct 2010 16:54:36 +0000 (16:54 +0000)]
added comments to test move of svn folder
svn path=/; revision=68
elserj [Thu, 14 Oct 2010 21:06:53 +0000 (21:06 +0000)]
Added script to take hal tree output and replace 2 char species names with full names
svn path=/; revision=67
preecej [Wed, 13 Oct 2010 00:47:00 +0000 (00:47 +0000)]
Added system call to sort the results file and remove exact dupes.
svn path=/; revision=66
preecej [Tue, 12 Oct 2010 00:30:43 +0000 (00:30 +0000)]
Added code for all mappings, statistical counters, and STDOUT; tested with
small data set that contained several intentional overlaps between
reactome and chebi terms
svn path=/; revision=65
preecej [Mon, 11 Oct 2010 17:24:19 +0000 (17:24 +0000)]
Removed unnecessary backups from laptop
svn path=/; revision=64
preecej [Mon, 11 Oct 2010 17:11:18 +0000 (17:11 +0000)]
Switched from Bio::OntologyIO module to GO::Parser (go-perl)
svn path=/; revision=63
preecej [Sat, 9 Oct 2010 07:21:33 +0000 (07:21 +0000)]
copying
svn path=/; revision=62
preecej [Sat, 9 Oct 2010 00:30:00 +0000 (00:30 +0000)]
wrote outline for sub perform_map(); successfully added code for mapping
on RiceCyc term name; added header line to output file
svn path=/; revision=61
preecej [Fri, 8 Oct 2010 19:30:50 +0000 (19:30 +0000)]
hash loads of CAS, LIGAND, RiceCyc
svn path=/; revision=60
preecej [Fri, 8 Oct 2010 00:51:38 +0000 (00:51 +0000)]
added individual hashes for each input type; attempted population of CAS
input hash; stubbed out main mapping algo
svn path=/; revision=59
preecej [Thu, 7 Oct 2010 20:50:44 +0000 (20:50 +0000)]
imported Bio::OntologyIO and ran parser test on CHEBI obo file
svn path=/; revision=58
preecej [Thu, 7 Oct 2010 00:43:56 +0000 (00:43 +0000)]
Basic stub-out of reactome::chebi mapping script.
svn path=/; revision=57
preecej [Wed, 6 Oct 2010 23:27:27 +0000 (23:27 +0000)]
Reactome::CHEBI mapping project
svn path=/; revision=56
elserj [Sat, 2 Oct 2010 00:03:30 +0000 (00:03 +0000)]
Fix require line to check for location of find_species.pl
svn path=/; revision=55
elserj [Sat, 2 Oct 2010 00:02:13 +0000 (00:02 +0000)]
Fix require line to check for location of find_species.pl
svn path=/; revision=54
elserj [Mon, 27 Sep 2010 23:26:34 +0000 (23:26 +0000)]
Fixed non-unique gene-id detection. Previous version only detected unique headers
svn path=/; revision=53
elserj [Mon, 27 Sep 2010 23:25:38 +0000 (23:25 +0000)]
Added detection of non-unique gene-ids
svn path=/; revision=52
elserj [Thu, 23 Sep 2010 22:02:41 +0000 (22:02 +0000)]
Fix gene header scope error and remove > symbol from gene header
svn path=/; revision=51
elserj [Thu, 23 Sep 2010 21:54:22 +0000 (21:54 +0000)]
Added species db loading script to svn. This script will parse the fasta files and put the gene_id, gene_header, and sequences into a database
svn path=/; revision=50
elserj [Thu, 23 Sep 2010 21:01:21 +0000 (21:01 +0000)]
Took out find_gene lookups as this will now be handled before inparanoid gets files. Fixes problem of blast incorrectly copying gene headers from fasta files
svn path=/; revision=49
elserj [Thu, 23 Sep 2010 20:54:56 +0000 (20:54 +0000)]
Change filename split so that errant dashes won't cause incorrect species lookups
svn path=/; revision=48
elserj [Thu, 23 Sep 2010 00:24:05 +0000 (00:24 +0000)]
Moved the "clusters" table select statement outside the loop. Fixes random stalls and improves performance (not by much)
svn path=/; revision=47
elserj [Thu, 23 Sep 2010 00:23:23 +0000 (00:23 +0000)]
Fix Pediculus gene identification
svn path=/; revision=46
elserj [Wed, 22 Sep 2010 20:38:56 +0000 (20:38 +0000)]
Fix whitespace and remove old comments
svn path=/; revision=45
elserj [Wed, 22 Sep 2010 20:24:02 +0000 (20:24 +0000)]
Exit script if wrong number of arguments is found
svn path=/; revision=44
elserj [Tue, 21 Sep 2010 23:17:18 +0000 (23:17 +0000)]
Run fasta_header_fix.pl on fasta files before submitting to queue
svn path=/; revision=43
elserj [Tue, 21 Sep 2010 22:49:19 +0000 (22:49 +0000)]
Added usage comment if wrong number of arguments
svn path=/; revision=42
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