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preecej [Fri, 5 Aug 2011 23:14:12 +0000 (23:14 +0000)]
Added MH's gene counting code, changed gene hash tp accept 1-to-many
mappings, removed Biopax publication nodes in output file using XML:DOM
svn path=/; revision=141
preecej [Fri, 5 Aug 2011 19:33:44 +0000 (19:33 +0000)]
Separated locus and accession id vars; made each more flexible.
svn path=/; revision=140
preecej [Wed, 3 Aug 2011 22:24:36 +0000 (22:24 +0000)]
Set seed values for fresh import.
svn path=/; revision=139
preecej [Wed, 3 Aug 2011 21:10:35 +0000 (21:10 +0000)]
Just keeping the wiki code current
svn path=/; revision=138
preecej [Wed, 3 Aug 2011 19:06:06 +0000 (19:06 +0000)]
added folder to hold "static" wiki content pages, such as the Main Page
svn path=/; revision=137
preecej [Mon, 1 Aug 2011 20:31:23 +0000 (20:31 +0000)]
Added GPML read-in, STDOUT/file out/manipulation tests.
svn path=/; revision=136
preecej [Sat, 30 Jul 2011 00:42:34 +0000 (00:42 +0000)]
Adds simple read-in of csv gene-swapping file
svn path=/; revision=135
preecej [Fri, 29 Jul 2011 23:54:56 +0000 (23:54 +0000)]
Updated just before migration to Test.
svn path=/; revision=134
preecej [Fri, 29 Jul 2011 23:52:30 +0000 (23:52 +0000)]
Added before migrating to Test.
svn path=/; revision=133
preecej [Fri, 29 Jul 2011 23:41:31 +0000 (23:41 +0000)]
Added the planteome skin, built from the vector skin
svn path=/; revision=132
preecej [Fri, 29 Jul 2011 23:32:24 +0000 (23:32 +0000)]
Latest version of paw forms, just before migration to Test env.
svn path=/; revision=131
preecej [Fri, 29 Jul 2011 22:36:33 +0000 (22:36 +0000)]
Completed GAF import transformation script for scale testing.
svn path=/; revision=130
preecej [Fri, 29 Jul 2011 01:42:52 +0000 (01:42 +0000)]
Began XML doc write using XML::Writer
svn path=/; revision=129
preecej [Thu, 28 Jul 2011 21:37:04 +0000 (21:37 +0000)]
Added commentary amd config file read-in
svn path=/; revision=128
preecej [Thu, 28 Jul 2011 18:39:11 +0000 (18:39 +0000)]
Includes Mamatha's first updates to opt args
svn path=/; revision=127
preecej [Thu, 28 Jul 2011 18:36:18 +0000 (18:36 +0000)]
Completed data read-in of GAF file (paw_TransformForImport.pl)
svn path=/; revision=126
preecej [Tue, 26 Jul 2011 17:39:25 +0000 (17:39 +0000)]
New script for directly modifying PathVisio GPML files - swaps one
species' genes for another (after projection)
svn path=/; revision=125
preecej [Mon, 25 Jul 2011 23:46:47 +0000 (23:46 +0000)]
Began breaking out GAF from generic CSV, tab format.
svn path=/; revision=124
preecej [Sat, 23 Jul 2011 00:47:37 +0000 (00:47 +0000)]
Started adding GAF format input option to Rev 0.2
svn path=/; revision=123
preecej [Tue, 19 Jul 2011 22:42:53 +0000 (22:42 +0000)]
Minor query updates to better handle obsolete terms
svn path=/; revision=122
preecej [Fri, 15 Jul 2011 18:24:00 +0000 (18:24 +0000)]
Added a max return count of 50, filtered out OBSOLETE terms and any
terms not affiliated with the two branches of the PO (anatomy, and
growth & development stages).
svn path=/; revision=121
preecej [Fri, 15 Jul 2011 18:11:15 +0000 (18:11 +0000)]
Modified queries to provide more fields from the AmiGO db.
svn path=/; revision=120
preecej [Wed, 13 Jul 2011 01:16:49 +0000 (01:16 +0000)]
new RESTful web service for the PO site and for the Planteome annotation
wiki
svn path=/; revision=119
elserj [Sat, 9 Jul 2011 00:44:57 +0000 (00:44 +0000)]
Update for new fasta files
svn path=/; revision=118
preecej [Fri, 8 Jul 2011 00:45:46 +0000 (00:45 +0000)]
Stashing local copies of LocalSettings.php for safekeeping
svn path=/; revision=117
elserj [Wed, 6 Jul 2011 23:58:36 +0000 (23:58 +0000)]
works now, at least for Spanish
svn path=/; revision=116
elserj [Wed, 6 Jul 2011 23:57:59 +0000 (23:57 +0000)]
Moved to DbiFloret::dbconnect for db connection, and put in some versioning info
svn path=/; revision=115
elserj [Wed, 6 Jul 2011 23:56:01 +0000 (23:56 +0000)]
Added new species
svn path=/; revision=114
elserj [Wed, 6 Jul 2011 23:53:02 +0000 (23:53 +0000)]
Switch to using dbconnect method from DbiFloret module
svn path=/; revision=113
elserj [Wed, 6 Jul 2011 23:46:23 +0000 (23:46 +0000)]
Fixed so that backspace works
svn path=/; revision=112
preecej [Wed, 6 Jul 2011 22:35:55 +0000 (22:35 +0000)]
xml file-generation debug
svn path=/; revision=111
preecej [Wed, 6 Jul 2011 22:15:00 +0000 (22:15 +0000)]
Changed name of import file from PS_* to paw_*
svn path=/; revision=110
preecej [Wed, 6 Jul 2011 00:23:43 +0000 (00:23 +0000)]
New version for dev.planteome.org. No changes yet.
svn path=/; revision=109
preecej [Fri, 1 Jul 2011 00:33:29 +0000 (00:33 +0000)]
More wiki source code.
svn path=/; revision=108
preecej [Fri, 1 Jul 2011 00:11:57 +0000 (00:11 +0000)]
Began storage of wiki forms and templates.
svn path=/; revision=107
elserj [Sun, 5 Jun 2011 16:47:11 +0000 (16:47 +0000)]
First version of translation insertion script, not working right yet
svn path=/; revision=106
preecej [Thu, 2 Jun 2011 20:48:20 +0000 (20:48 +0000)]
Completed first working version.
svn path=/; revision=105
preecej [Sat, 28 May 2011 01:05:18 +0000 (01:05 +0000)]
Added more provenance xml
svn path=/; revision=104
preecej [Sat, 28 May 2011 00:59:18 +0000 (00:59 +0000)]
Added input data viewing, started xml doc construction
svn path=/; revision=103
preecej [Fri, 27 May 2011 00:46:15 +0000 (00:46 +0000)]
Added input reads and tests
svn path=/; revision=102
preecej [Thu, 26 May 2011 04:07:22 +0000 (04:07 +0000)]
Initial pseudo-coding of PS import script
svn path=/; revision=101
preecej [Wed, 25 May 2011 19:54:01 +0000 (19:54 +0000)]
svn path=/; revision=100
preecej [Tue, 24 May 2011 00:28:13 +0000 (00:28 +0000)]
Added initial copy of DataTransfer extension, with intent to extend and
modify.
svn path=/; revision=99
preecej [Mon, 23 May 2011 23:41:20 +0000 (23:41 +0000)]
svn path=/; revision=98
preecej [Mon, 23 May 2011 22:57:19 +0000 (22:57 +0000)]
svn path=/; revision=97
preecej [Mon, 23 May 2011 22:51:34 +0000 (22:51 +0000)]
svn path=/; revision=96
preecej [Mon, 23 May 2011 22:08:16 +0000 (22:08 +0000)]
svn path=/; revision=95
preecej [Mon, 23 May 2011 22:06:27 +0000 (22:06 +0000)]
Refreshed versions of LocalSettings.php and NCBI_eDocSummary.php
svn path=/; revision=94
elserj [Wed, 4 May 2011 17:55:20 +0000 (17:55 +0000)]
Add check for .txt assoc files
svn path=/; revision=93
elserj [Wed, 4 May 2011 17:51:43 +0000 (17:51 +0000)]
Add file to create a fasta protein file from a list of genes
svn path=/; revision=92
preecej [Tue, 19 Apr 2011 20:16:18 +0000 (20:16 +0000)]
Added step-interaction data type and format converter script
svn path=/; revision=91
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
projects / old-jaiswallab-svn / .git / log