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elserj [Thu, 14 May 2015 21:25:37 +0000 (21:25 +0000)]
Testing write access
svn path=/; revision=624
elserj [Thu, 14 May 2015 18:32:28 +0000 (18:32 +0000)]
Added folder for Chris's temperature logger
svn path=/; revision=623
elserj [Mon, 27 Apr 2015 23:33:30 +0000 (23:33 +0000)]
New script that creates a fasta file with no isoforms. To be used in CAFE pipeline.
svn path=/; revision=622
elserj [Fri, 20 Feb 2015 20:21:50 +0000 (20:21 +0000)]
Fix Ectocarpus field separator
svn path=/; revision=621
elserj [Thu, 19 Feb 2015 23:06:01 +0000 (23:06 +0000)]
Script that will use supercluster table to generate fasta file with only longest (or random) genes from each cluster. Useful for running bio-hal
svn path=/; revision=620
albader [Thu, 19 Feb 2015 19:01:08 +0000 (19:01 +0000)]
updated assembly scripts $ test
svn path=/; revision=619
albader [Thu, 19 Feb 2015 18:36:19 +0000 (18:36 +0000)]
full assembly script-Chia
svn path=/; revision=618
albader [Wed, 18 Feb 2015 21:39:14 +0000 (21:39 +0000)]
test comment
svn path=/; revision=617
albader [Wed, 18 Feb 2015 21:28:26 +0000 (21:28 +0000)]
adding my first shell scripts for chia (round 1)
svn path=/; revision=616
albader [Wed, 18 Feb 2015 21:20:00 +0000 (21:20 +0000)]
my new Personnel folder for holding scripts
svn path=/; revision=615
elserj [Tue, 17 Feb 2015 18:00:10 +0000 (18:00 +0000)]
Add progress indicator
svn path=/; revision=614
elserj [Tue, 17 Feb 2015 00:41:57 +0000 (00:41 +0000)]
Add section that skips T.cacao transcripts
svn path=/; revision=613
elserj [Tue, 17 Feb 2015 00:15:21 +0000 (00:15 +0000)]
Added species hash list to check against and will only fix lines that match
svn path=/; revision=612
elserj [Mon, 16 Feb 2015 23:57:49 +0000 (23:57 +0000)]
Fix monococcum field separators
svn path=/; revision=611
elserj [Mon, 16 Feb 2015 23:56:25 +0000 (23:56 +0000)]
T.cacao genes <=> symbols
svn path=/; revision=610
elserj [Mon, 16 Feb 2015 23:52:59 +0000 (23:52 +0000)]
Fix Cannabis field seperator
svn path=/; revision=609
elserj [Mon, 16 Feb 2015 23:51:13 +0000 (23:51 +0000)]
Script that can fix InParanoid sqltable files that have incorrect gene ids
svn path=/; revision=608
elserj [Mon, 16 Feb 2015 22:36:46 +0000 (22:36 +0000)]
Fix incorrect separator for T.cacao
svn path=/; revision=607
elserj [Mon, 16 Feb 2015 22:24:22 +0000 (22:24 +0000)]
Fix a couple more incorrect gene names
svn path=/; revision=606
elserj [Mon, 16 Feb 2015 21:55:49 +0000 (21:55 +0000)]
Fix broken synonyms for Glycine max
svn path=/; revision=605
elserj [Mon, 16 Feb 2015 21:34:34 +0000 (21:34 +0000)]
Fix incorrect C.elegans gene names
svn path=/; revision=604
elserj [Wed, 11 Feb 2015 22:41:53 +0000 (22:41 +0000)]
Fix misspelling
svn path=/; revision=603
elserj [Wed, 11 Feb 2015 21:29:45 +0000 (21:29 +0000)]
Fix misspellings and shorten B.sylvaticum.Corvallis so that MySQL tables can be generated
svn path=/; revision=602
elserj [Fri, 6 Feb 2015 19:19:22 +0000 (19:19 +0000)]
Shorten B.sylvaticum.Corvallis name so that database table names are < 64 chars
svn path=/; revision=601
elserj [Fri, 6 Feb 2015 17:32:21 +0000 (17:32 +0000)]
Add error checking for db creation statement
svn path=/; revision=600
elserj [Sat, 10 Jan 2015 19:55:49 +0000 (19:55 +0000)]
Proper detection on lines that only contain a *
svn path=/; revision=599
elserj [Tue, 16 Dec 2014 23:46:49 +0000 (23:46 +0000)]
Scripts that can be used together to run inParanoid as an SGE batch array style job, also removes files after completion except for sqltable files which is moved to sqltables directory
svn path=/; revision=598
elserj [Tue, 16 Dec 2014 23:38:23 +0000 (23:38 +0000)]
Switch to using DBIFloret
svn path=/; revision=597
elserj [Tue, 16 Dec 2014 23:36:44 +0000 (23:36 +0000)]
Add synonym entries
svn path=/; revision=596
elserj [Tue, 16 Dec 2014 23:35:39 +0000 (23:35 +0000)]
Fix file handle name and wildcard db query
svn path=/; revision=595
elserj [Tue, 16 Dec 2014 23:34:40 +0000 (23:34 +0000)]
Fix split on tab
svn path=/; revision=594
elserj [Tue, 16 Dec 2014 23:34:12 +0000 (23:34 +0000)]
Add source and progress indicator
svn path=/; revision=593
elserj [Tue, 16 Dec 2014 23:33:24 +0000 (23:33 +0000)]
Generalize species input so that script doesn't have to be edited each time
svn path=/; revision=592
elserj [Tue, 16 Dec 2014 23:31:23 +0000 (23:31 +0000)]
Updated to work with all species in the 9_9_13 folder. Current as of 12-16-2014
svn path=/; revision=591
elserj [Tue, 16 Dec 2014 23:30:33 +0000 (23:30 +0000)]
Use proper file handles, add a die if can't open file for writing
svn path=/; revision=590
preecej [Wed, 29 Oct 2014 18:27:41 +0000 (18:27 +0000)]
updates for JBMS MS
svn path=/; revision=589
preecej [Wed, 29 Oct 2014 18:09:39 +0000 (18:09 +0000)]
updates for JBMS MS
svn path=/; revision=588
preecej [Wed, 29 Oct 2014 18:05:41 +0000 (18:05 +0000)]
updates for JBMS MS
svn path=/; revision=587
preecej [Wed, 29 Oct 2014 18:01:04 +0000 (18:01 +0000)]
updates for JBMS MS
svn path=/; revision=586
preecej [Tue, 28 Oct 2014 22:57:50 +0000 (22:57 +0000)]
updates for AISO JBMS MS
svn path=/; revision=585
preecej [Tue, 28 Oct 2014 22:29:37 +0000 (22:29 +0000)]
updates for AISO JBMS MS
svn path=/; revision=584
preecej [Tue, 28 Oct 2014 22:15:28 +0000 (22:15 +0000)]
AISO MS updates
svn path=/; revision=583
preecej [Tue, 28 Oct 2014 22:11:37 +0000 (22:11 +0000)]
edits to align with instructions in AISO manuscript
svn path=/; revision=582
preecej [Tue, 12 Aug 2014 23:44:10 +0000 (23:44 +0000)]
The generation of the MSU-RAP dictionary now accepts .2, .3, .4, etc.
isoforms if no .1 is present. This will ensure the inclusion of more
orthology mappings.
svn path=/; revision=581
elserj [Mon, 11 Aug 2014 18:03:41 +0000 (18:03 +0000)]
Fixed species names with dots or commas in names
svn path=/; revision=580
elserj [Tue, 22 Jul 2014 22:42:49 +0000 (22:42 +0000)]
Added species
svn path=/; revision=579
preecej [Thu, 3 Jul 2014 00:31:34 +0000 (00:31 +0000)]
...and the post-exercise script for 1.pl
svn path=/; revision=578
preecej [Thu, 3 Jul 2014 00:29:30 +0000 (00:29 +0000)]
Added STEM 2014 camp scripts. Draft stage.
svn path=/; revision=577
elserj [Thu, 12 Jun 2014 23:14:14 +0000 (23:14 +0000)]
Added code that generates the actual venn diagram images. Needs source files with outlines to work, also in this commit in the Personnel/elserj/venn_sources folder
svn path=/; revision=576
preecej [Tue, 15 Apr 2014 19:06:55 +0000 (19:06 +0000)]
diagram conditional size adjustment
svn path=/; revision=575
preecej [Tue, 15 Apr 2014 19:05:23 +0000 (19:05 +0000)]
added percentage coverage comparisons, more captioning on diagrams
svn path=/; revision=574
preecej [Mon, 14 Apr 2014 23:19:58 +0000 (23:19 +0000)]
now saves Venn figure files as PNG (and also generates projection Venn
diagrams
svn path=/; revision=573
preecej [Mon, 14 Apr 2014 19:16:41 +0000 (19:16 +0000)]
enhanced Venn args, wip: projection diagram
svn path=/; revision=572
preecej [Fri, 11 Apr 2014 21:37:35 +0000 (21:37 +0000)]
added Venn generator
svn path=/; revision=571
preecej [Thu, 10 Apr 2014 17:15:45 +0000 (17:15 +0000)]
wip: venn diagram output
svn path=/; revision=570
preecej [Sat, 5 Apr 2014 01:41:47 +0000 (01:41 +0000)]
complete refactor of projection comparison code; added more projection
stats
svn path=/; revision=569
preecej [Fri, 4 Apr 2014 01:36:45 +0000 (01:36 +0000)]
added ensembl confidence flag
svn path=/; revision=568
preecej [Wed, 2 Apr 2014 20:40:17 +0000 (20:40 +0000)]
now generates optional reactome projection output files
svn path=/; revision=567
preecej [Wed, 2 Apr 2014 00:14:21 +0000 (00:14 +0000)]
wip: joining list of projections and prefixing at same time
svn path=/; revision=566
preecej [Sat, 29 Mar 2014 03:00:44 +0000 (03:00 +0000)]
wip
svn path=/; revision=565
preecej [Sat, 29 Mar 2014 02:58:03 +0000 (02:58 +0000)]
wip: reactome output files
svn path=/; revision=564
preecej [Fri, 28 Mar 2014 00:48:01 +0000 (00:48 +0000)]
wip: generate_reactome_files option
svn path=/; revision=563
preecej [Fri, 28 Mar 2014 00:43:55 +0000 (00:43 +0000)]
added projection prefix option
svn path=/; revision=562
preecej [Wed, 26 Mar 2014 01:04:47 +0000 (01:04 +0000)]
finished optional uniprot mapping
svn path=/; revision=561
preecej [Tue, 25 Mar 2014 00:00:54 +0000 (00:00 +0000)]
wip: uniprot substitution for ref loci
svn path=/; revision=560
preecej [Sat, 22 Mar 2014 00:38:05 +0000 (00:38 +0000)]
major revision completed: now accepts all input as file args and
generates output files
svn path=/; revision=559
pankaj [Fri, 21 Mar 2014 20:23:03 +0000 (20:23 +0000)]
text edits
svn path=/; revision=558
pankaj [Fri, 21 Mar 2014 20:06:47 +0000 (20:06 +0000)]
fixed superscripts identifying source: gramene, naithani and jaiswal labs
svn path=/; revision=557
preecej [Fri, 21 Mar 2014 17:05:01 +0000 (17:05 +0000)]
rename program to make it more generic
svn path=/; revision=556
elserj [Fri, 21 Mar 2014 00:57:31 +0000 (00:57 +0000)]
Updated version numbers to match pathway tools 18.0
svn path=/; revision=555
preecej [Fri, 21 Mar 2014 00:15:02 +0000 (00:15 +0000)]
WIP, not building at the moment. refactoring to accept ens, inp super
cluster, and rap map files all at once, run in one shot, produce
mapping and overlap stats files. future work: also produce reactome
orthopair files and venne diagram. maybe build UI, too, just to learn
how.
svn path=/; revision=554
pankaj [Thu, 20 Mar 2014 22:28:43 +0000 (22:28 +0000)]
svn path=/; revision=553
pankaj [Thu, 20 Mar 2014 22:27:48 +0000 (22:27 +0000)]
svn path=/; revision=552
pankaj [Thu, 20 Mar 2014 22:26:55 +0000 (22:26 +0000)]
added image link for logo
svn path=/; revision=551
pankaj [Thu, 20 Mar 2014 22:23:32 +0000 (22:23 +0000)]
pathways website logo
svn path=/; revision=550
pankaj [Thu, 20 Mar 2014 21:59:51 +0000 (21:59 +0000)]
spell check and rephrased the metabolic.html link
svn path=/; revision=549
pankaj [Thu, 20 Mar 2014 21:57:47 +0000 (21:57 +0000)]
added fragaria
svn path=/; revision=548
pankaj [Thu, 20 Mar 2014 21:55:44 +0000 (21:55 +0000)]
updated the content
svn path=/; revision=547
pankaj [Thu, 20 Mar 2014 21:53:59 +0000 (21:53 +0000)]
added addition Cycs and updated hyperlinks
svn path=/; revision=546
pankaj [Thu, 20 Mar 2014 21:49:34 +0000 (21:49 +0000)]
fragariacyc logo
svn path=/; revision=545
pankaj [Thu, 20 Mar 2014 21:46:13 +0000 (21:46 +0000)]
eucalypcyc logo
svn path=/; revision=544
pankaj [Thu, 20 Mar 2014 21:40:37 +0000 (21:40 +0000)]
vitiscyc logo
svn path=/; revision=543
pankaj [Thu, 20 Mar 2014 21:06:45 +0000 (21:06 +0000)]
metabolic pathway database and species listing
svn path=/; revision=542
pankaj [Thu, 20 Mar 2014 20:14:09 +0000 (20:14 +0000)]
added image folder
svn path=/; revision=541
pankaj [Thu, 20 Mar 2014 17:47:36 +0000 (17:47 +0000)]
test changes
svn path=/; revision=540
elserj [Thu, 20 Mar 2014 17:40:19 +0000 (17:40 +0000)]
Added pathways website folder for Pankaj with shell index.html
svn path=/; revision=539
elserj [Fri, 14 Mar 2014 23:26:03 +0000 (23:26 +0000)]
Added Triticum turgidum
svn path=/; revision=538
elserj [Fri, 14 Mar 2014 00:43:09 +0000 (00:43 +0000)]
Fixed Zea and added new species
svn path=/; revision=537
preecej [Tue, 11 Mar 2014 21:09:58 +0000 (21:09 +0000)]
Performance improvement. Changed dictionary lookup from...
if item in dict.keys() :
to...
if item in dict :
Noticeably faster.
svn path=/; revision=536
preecej [Sat, 8 Mar 2014 01:29:10 +0000 (01:29 +0000)]
mods for projected species flexibility
svn path=/; revision=535
preecej [Sat, 8 Mar 2014 01:07:05 +0000 (01:07 +0000)]
major development complete; now testing w/ different projected species
svn path=/; revision=534
preecej [Fri, 7 Mar 2014 18:03:42 +0000 (18:03 +0000)]
completed first draft of ensembl projection 50% reciprocal id mappings
svn path=/; revision=533
preecej [Fri, 7 Mar 2014 00:27:19 +0000 (00:27 +0000)]
wip
svn path=/; revision=532
preecej [Wed, 5 Mar 2014 01:18:28 +0000 (01:18 +0000)]
draft of os loc 2 at mapping mashup
svn path=/; revision=531
preecej [Wed, 5 Mar 2014 00:25:08 +0000 (00:25 +0000)]
svn path=/; revision=530
elserj [Thu, 20 Feb 2014 17:51:19 +0000 (17:51 +0000)]
Fixed incorrect mays gene naming
svn path=/; revision=529
elserj [Sat, 15 Feb 2014 00:23:51 +0000 (00:23 +0000)]
Added 4 new Oryza species from Pankaj
svn path=/; revision=528
elserj [Fri, 14 Feb 2014 17:40:36 +0000 (17:40 +0000)]
Updated for new species and fixed a couple of regex issues
svn path=/; revision=527
patapanp [Mon, 10 Feb 2014 21:56:15 +0000 (21:56 +0000)]
svn path=/; revision=526
patapanp [Mon, 3 Feb 2014 20:24:17 +0000 (20:24 +0000)]
Combined label is changed to Segmented Sucessfuly.
svn path=/; revision=525
projects / old-jaiswallab-svn / .git / log