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elserj [Mon, 26 Aug 2019 22:41:36 +0000 (22:41 +0000)]
Change to using isoform_info from protein_sequences for a count of only canonical genes
svn path=/; revision=666
elserj [Sun, 25 Aug 2019 18:14:46 +0000 (18:14 +0000)]
Update to include canonical transcript counts when loading protein
sequences
svn path=/; revision=665
elserj [Tue, 14 May 2019 22:01:59 +0000 (22:01 +0000)]
Fix couple of entries for taxons
svn path=/; revision=664
elserj [Tue, 14 May 2019 21:55:22 +0000 (21:55 +0000)]
Script to generate fasta_taxon_mapping.txt file for iprscan
svn path=/; revision=663
elserj [Fri, 8 Mar 2019 19:08:40 +0000 (19:08 +0000)]
Fix O. sativa Aus kasalath
svn path=/; revision=662
elserj [Fri, 1 Mar 2019 21:13:23 +0000 (21:13 +0000)]
Add dbconnect_local subroutine
svn path=/; revision=661
elserj [Fri, 1 Mar 2019 21:03:05 +0000 (21:03 +0000)]
Add dot (.) to regex so that fasta files with them don't error
svn path=/; revision=660
elserj [Fri, 1 Mar 2019 20:59:22 +0000 (20:59 +0000)]
Add new species and subroutines to use for common mart and ensembl downloads
svn path=/; revision=659
elserj [Fri, 1 Mar 2019 20:57:30 +0000 (20:57 +0000)]
New Zea mays genes have additional padding 0 in transcript id
svn path=/; revision=658
elserj [Tue, 27 Mar 2018 22:12:24 +0000 (22:12 +0000)]
Fix typo
svn path=/; revision=657
elserj [Tue, 27 Mar 2018 22:02:10 +0000 (22:02 +0000)]
Fix broken synonyms inserts
svn path=/; revision=656
elserj [Fri, 21 Apr 2017 22:33:09 +0000 (22:33 +0000)]
Add script that will look for known isoform patterns and create a new fasta file without them
svn path=/; revision=655
elserj [Wed, 28 Dec 2016 20:50:08 +0000 (20:50 +0000)]
Add more beavers
svn path=/; revision=654
elserj [Fri, 23 Dec 2016 01:09:34 +0000 (01:09 +0000)]
Add more beaver
svn path=/; revision=653
elserj [Fri, 9 Dec 2016 17:29:57 +0000 (17:29 +0000)]
Remove deprecated TYPE from sql table creation
svn path=/; revision=652
elserj [Fri, 9 Dec 2016 17:27:32 +0000 (17:27 +0000)]
Add weighted version of supercluster program
svn path=/; revision=651
elserj [Tue, 6 Dec 2016 22:28:27 +0000 (22:28 +0000)]
Add beaver no-isoforms
svn path=/; revision=650
elserj [Thu, 1 Dec 2016 03:53:32 +0000 (03:53 +0000)]
Fix a couple of typos
svn path=/; revision=649
elserj [Thu, 1 Dec 2016 03:42:09 +0000 (03:42 +0000)]
Fix Mustela putorius sub species
svn path=/; revision=648
elserj [Thu, 1 Dec 2016 03:27:38 +0000 (03:27 +0000)]
Add new mammal species
svn path=/; revision=647
elserj [Thu, 10 Nov 2016 00:18:45 +0000 (00:18 +0000)]
Add aiso xml parsing script. Runs over zip files in current directory and adds them to floret/image_annotation msyql.
svn path=/; revision=646
elserj [Tue, 18 Oct 2016 17:57:09 +0000 (17:57 +0000)]
Add Gossypium hirsutum
svn path=/; revision=645
preecej [Wed, 23 Mar 2016 01:28:28 +0000 (01:28 +0000)]
now handles direct RAP::UniProt mapping for Ensembl data, not just
RAP:MSU:UniProt. more inclusive
svn path=/; revision=644
elserj [Thu, 10 Mar 2016 21:42:40 +0000 (21:42 +0000)]
Input species order no longer matters. Added extra argument to make it detect which species to search for in sql statement
svn path=/; revision=643
elserj [Mon, 28 Dec 2015 23:02:45 +0000 (23:02 +0000)]
Added taxon lookup table
svn path=/; revision=642
elserj [Thu, 3 Dec 2015 01:20:45 +0000 (01:20 +0000)]
Fixed all bugs and also now outputs the lines to a set of files. Probably should find a better way to name the output files, but can be changed later.
svn path=/; revision=641
elserj [Wed, 2 Dec 2015 22:52:47 +0000 (22:52 +0000)]
Remove unneeded variable that was there from testing
svn path=/; revision=640
elserj [Wed, 2 Dec 2015 22:46:19 +0000 (22:46 +0000)]
Found bug in loop over file 2 hash. Was counting some twice because of it.
svn path=/; revision=639
elserj [Wed, 2 Dec 2015 22:29:33 +0000 (22:29 +0000)]
Initial version of SNP venn statistics script
svn path=/; revision=638
elserj [Tue, 20 Oct 2015 22:21:09 +0000 (22:21 +0000)]
Fix spelling of Arachis duranensis and add two Salvia species for Matt
svn path=/; revision=637
elserj [Tue, 20 Oct 2015 00:46:08 +0000 (00:46 +0000)]
Add check to see if table exists, and skip ahead if it doesn't
svn path=/; revision=636
elserj [Thu, 8 Oct 2015 21:55:39 +0000 (21:55 +0000)]
Added new bean species, Arachis_duramensis, Arachis_ipaensis, Phaseolus_vulgaris
svn path=/; revision=635
elserj [Wed, 23 Sep 2015 22:29:02 +0000 (22:29 +0000)]
Script that will generate the tabulated cluster gene counts from InParanoid. To be used with cafe instead of using MPIBlast/MCL to calculate.
svn path=/; revision=634
elserj [Fri, 4 Sep 2015 21:09:36 +0000 (21:09 +0000)]
Took out _longest_ from file name, don't really need it and was just forcing me to rename files after
svn path=/; revision=633
elserj [Fri, 4 Sep 2015 18:49:01 +0000 (18:49 +0000)]
Added script that takes a species list and copies only relevant sqltable files (from inparanoid) to a new directory
svn path=/; revision=632
elserj [Fri, 28 Aug 2015 21:31:07 +0000 (21:31 +0000)]
Added Kalanchoe laxiflora
svn path=/; revision=631
elserj [Thu, 28 May 2015 00:08:52 +0000 (00:08 +0000)]
Added section to parse OBO files in addition to assoc files for taxon IDs
svn path=/; revision=630
elserj [Fri, 22 May 2015 21:32:36 +0000 (21:32 +0000)]
Added script that parses NCBI taxonomy.dat file and creates slim OWL file, to be used by planteome.
svn path=/; revision=629
elserj [Fri, 22 May 2015 21:32:14 +0000 (21:32 +0000)]
Testing
svn path=/; revision=628
elserj [Thu, 14 May 2015 22:44:01 +0000 (22:44 +0000)]
Testing
svn path=/; revision=627
elserj [Thu, 14 May 2015 22:29:09 +0000 (22:29 +0000)]
Testing
svn path=/; revision=626
elserj [Thu, 14 May 2015 22:17:20 +0000 (22:17 +0000)]
Remove test directory
svn path=/; revision=625
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
projects / old-jaiswallab-svn / .git / log