function2gene.git
11 years agoskip ENSG results, and use average weight
Don Armstrong [Thu, 28 Feb 2008 02:18:23 +0000 (02:18 +0000)]
skip ENSG results, and use average weight

git-svn-id: file:///srv/svn/function2gene/trunk@38 a0738b58-4706-0410-8799-fb830574a030

11 years ago * Default back to ncbi genecards and harvester, but indicate that ensembl and unipro...
Don Armstrong [Wed, 27 Feb 2008 22:36:27 +0000 (22:36 +0000)]
 * Default back to ncbi genecards and harvester, but indicate that ensembl and uniprot are also supported

git-svn-id: file:///srv/svn/function2gene/trunk@37 a0738b58-4706-0410-8799-fb830574a030

11 years agohandle combining based on aliases better; adjust autoweight
Don Armstrong [Tue, 26 Feb 2008 01:09:08 +0000 (01:09 +0000)]
handle combining based on aliases better; adjust autoweight

git-svn-id: file:///srv/svn/function2gene/trunk@36 a0738b58-4706-0410-8799-fb830574a030

11 years agoskip unreviewed and fragment records
Don Armstrong [Tue, 26 Feb 2008 01:08:51 +0000 (01:08 +0000)]
skip unreviewed and fragment records

git-svn-id: file:///srv/svn/function2gene/trunk@35 a0738b58-4706-0410-8799-fb830574a030

11 years agoupdate function2gene to allow uniprot
Don Armstrong [Mon, 25 Feb 2008 23:19:23 +0000 (23:19 +0000)]
update function2gene to allow uniprot

git-svn-id: file:///srv/svn/function2gene/trunk@34 a0738b58-4706-0410-8799-fb830574a030

11 years agoadd get and parse uniprot results
Don Armstrong [Mon, 25 Feb 2008 23:18:43 +0000 (23:18 +0000)]
add get and parse uniprot results

git-svn-id: file:///srv/svn/function2gene/trunk@33 a0738b58-4706-0410-8799-fb830574a030

11 years agoadd todo
Don Armstrong [Thu, 14 Feb 2008 05:55:29 +0000 (05:55 +0000)]
add todo

git-svn-id: file:///srv/svn/function2gene/trunk@32 a0738b58-4706-0410-8799-fb830574a030

11 years ago * Finish addition of ensembl support
Don Armstrong [Thu, 14 Feb 2008 05:55:09 +0000 (05:55 +0000)]
 * Finish addition of ensembl support

git-svn-id: file:///srv/svn/function2gene/trunk@31 a0738b58-4706-0410-8799-fb830574a030

11 years agoadd parse ensembl results
Don Armstrong [Thu, 14 Feb 2008 02:08:05 +0000 (02:08 +0000)]
add parse ensembl results

git-svn-id: file:///srv/svn/function2gene/trunk@30 a0738b58-4706-0410-8799-fb830574a030

11 years agoadd get_ensembl_results
Don Armstrong [Thu, 14 Feb 2008 00:07:54 +0000 (00:07 +0000)]
add get_ensembl_results

git-svn-id: file:///srv/svn/function2gene/trunk@29 a0738b58-4706-0410-8799-fb830574a030

11 years agohandle \r properly
Don Armstrong [Fri, 25 Jan 2008 03:01:42 +0000 (03:01 +0000)]
handle \r properly

git-svn-id: file:///srv/svn/function2gene/trunk@28 a0738b58-4706-0410-8799-fb830574a030

11 years ago * Update readme
Don Armstrong [Wed, 23 Jan 2008 01:11:39 +0000 (01:11 +0000)]
 * Update readme

git-svn-id: file:///srv/svn/function2gene/trunk@27 a0738b58-4706-0410-8799-fb830574a030

11 years ago * Stop requiring wget
Don Armstrong [Tue, 22 Jan 2008 23:04:20 +0000 (23:04 +0000)]
 * Stop requiring wget
 * Fix issue with file naming after not requiring wget
 * Fix undefined warning in combine_results

git-svn-id: file:///srv/svn/function2gene/trunk@26 a0738b58-4706-0410-8799-fb830574a030

11 years ago * Update readme
Don Armstrong [Tue, 15 Jan 2008 00:04:14 +0000 (00:04 +0000)]
 * Update readme

git-svn-id: file:///srv/svn/function2gene/trunk@25 a0738b58-4706-0410-8799-fb830574a030

11 years agostart working towards supporting keyword weights
Don Armstrong [Thu, 13 Dec 2007 02:31:46 +0000 (02:31 +0000)]
start working towards supporting keyword weights

git-svn-id: file:///srv/svn/function2gene/trunk@24 a0738b58-4706-0410-8799-fb830574a030

11 years ago * Start supporting keyword weights
Don Armstrong [Thu, 13 Dec 2007 02:31:32 +0000 (02:31 +0000)]
 * Start supporting keyword weights
 * Transition from do_it_all_state to function2gene_state
 * Fix invalidate_state function to invalidate state dependencies

git-svn-id: file:///srv/svn/function2gene/trunk@23 a0738b58-4706-0410-8799-fb830574a030

11 years agohandle new genecards site
Don Armstrong [Thu, 13 Dec 2007 02:30:36 +0000 (02:30 +0000)]
handle new genecards site

git-svn-id: file:///srv/svn/function2gene/trunk@22 a0738b58-4706-0410-8799-fb830574a030

11 years ago * Add --invalidate-state option to specifically invalidate a state
Don Armstrong [Wed, 12 Dec 2007 00:42:08 +0000 (00:42 +0000)]
 * Add --invalidate-state option to specifically invalidate a state

git-svn-id: file:///srv/svn/function2gene/trunk@21 a0738b58-4706-0410-8799-fb830574a030

11 years ago * Fix "rety" typo
Don Armstrong [Wed, 12 Dec 2007 00:29:18 +0000 (00:29 +0000)]
 * Fix "rety" typo

git-svn-id: file:///srv/svn/function2gene/trunk@20 a0738b58-4706-0410-8799-fb830574a030

11 years ago * Handle when NCBI has remote server errors "gracefully"
Don Armstrong [Wed, 12 Dec 2007 00:28:41 +0000 (00:28 +0000)]
 * Handle when NCBI has remote server errors "gracefully"
 * Fix pubmed/ncbi typo

git-svn-id: file:///srv/svn/function2gene/trunk@19 a0738b58-4706-0410-8799-fb830574a030

11 years agomodify readme some more; add Makefile.PL
Don Armstrong [Tue, 4 Dec 2007 02:04:04 +0000 (02:04 +0000)]
modify readme some more; add Makefile.PL

git-svn-id: file:///srv/svn/function2gene/trunk@18 a0738b58-4706-0410-8799-fb830574a030

11 years agoadd a readme
Don Armstrong [Sun, 4 Nov 2007 04:47:05 +0000 (04:47 +0000)]
add a readme

git-svn-id: file:///srv/svn/function2gene/trunk@17 a0738b58-4706-0410-8799-fb830574a030

11 years agoremove useless lib directory
Don Armstrong [Sat, 27 Oct 2007 00:15:10 +0000 (00:15 +0000)]
remove useless lib directory

git-svn-id: file:///srv/svn/function2gene/trunk@16 a0738b58-4706-0410-8799-fb830574a030

11 years ago * Fix genecard and harvester parsers
Don Armstrong [Sat, 27 Oct 2007 00:14:42 +0000 (00:14 +0000)]
 * Fix genecard and harvester parsers
 * Add headers for results_to_table
 * Call results_to_table in function2gene

git-svn-id: file:///srv/svn/function2gene/trunk@15 a0738b58-4706-0410-8799-fb830574a030

11 years agoAdd results to table; modify the search parssers to work better. Fix error in get_ncb...
Don Armstrong [Fri, 26 Oct 2007 21:40:13 +0000 (21:40 +0000)]
Add results to table; modify the search parssers to work better. Fix error in get_ncbi_results

git-svn-id: file:///srv/svn/function2gene/trunk@14 a0738b58-4706-0410-8799-fb830574a030

11 years ago * Rename do_it_all; document function2gene more clearly
Don Armstrong [Fri, 26 Oct 2007 20:26:45 +0000 (20:26 +0000)]
 * Rename do_it_all; document function2gene more clearly

git-svn-id: file:///srv/svn/function2gene/trunk@13 a0738b58-4706-0410-8799-fb830574a030

11 years agoupdate combine results
Don Armstrong [Fri, 26 Oct 2007 01:07:43 +0000 (01:07 +0000)]
update combine results

git-svn-id: file:///srv/svn/function2gene/trunk@12 a0738b58-4706-0410-8799-fb830574a030

11 years agoupdate everything again
Don Armstrong [Tue, 28 Aug 2007 02:54:48 +0000 (02:54 +0000)]
update everything again

git-svn-id: file:///srv/svn/function2gene/trunk@11 a0738b58-4706-0410-8799-fb830574a030

11 years agohandle command failure; fix write_command_to_file
Don Armstrong [Tue, 28 Aug 2007 01:02:26 +0000 (01:02 +0000)]
handle command failure; fix write_command_to_file

git-svn-id: file:///srv/svn/function2gene/trunk@10 a0738b58-4706-0410-8799-fb830574a030

11 years agoupdate get harvester results for new site
Don Armstrong [Tue, 28 Aug 2007 01:01:57 +0000 (01:01 +0000)]
update get harvester results for new site

git-svn-id: file:///srv/svn/function2gene/trunk@9 a0738b58-4706-0410-8799-fb830574a030

11 years agoupdate copyright information
Don Armstrong [Tue, 28 Aug 2007 01:01:28 +0000 (01:01 +0000)]
update copyright information

git-svn-id: file:///srv/svn/function2gene/trunk@8 a0738b58-4706-0410-8799-fb830574a030

11 years ago * Update ncbi results to handle the new ncbi output format
Don Armstrong [Tue, 28 Aug 2007 01:00:57 +0000 (01:00 +0000)]
 * Update ncbi results to handle the new ncbi output format

git-svn-id: file:///srv/svn/function2gene/trunk@7 a0738b58-4706-0410-8799-fb830574a030

11 years agomove get_ncbi_results
Don Armstrong [Mon, 27 Aug 2007 22:29:47 +0000 (22:29 +0000)]
move get_ncbi_results

git-svn-id: file:///srv/svn/function2gene/trunk@6 a0738b58-4706-0410-8799-fb830574a030

11 years agoupdate search program with options for do_it_all; implement calls to subsideary scripts
Don Armstrong [Mon, 27 Aug 2007 22:29:21 +0000 (22:29 +0000)]
update search program with options for do_it_all; implement calls to subsideary scripts

git-svn-id: file:///srv/svn/function2gene/trunk@5 a0738b58-4706-0410-8799-fb830574a030

11 years agoadd threads implementation to actually handle doing the useful stuff
Don Armstrong [Sat, 25 Aug 2007 02:23:41 +0000 (02:23 +0000)]
add threads implementation to actually handle doing the useful stuff

git-svn-id: file:///srv/svn/function2gene/trunk@4 a0738b58-4706-0410-8799-fb830574a030

11 years agoadd do it all script to call other modules
Don Armstrong [Fri, 24 Aug 2007 09:12:28 +0000 (09:12 +0000)]
add do it all script to call other modules

git-svn-id: file:///srv/svn/function2gene/trunk@3 a0738b58-4706-0410-8799-fb830574a030

12 years agoadd bin files for search routines
Don Armstrong [Sat, 12 May 2007 05:23:43 +0000 (05:23 +0000)]
add bin files for search routines

git-svn-id: file:///srv/svn/function2gene/trunk@2 a0738b58-4706-0410-8799-fb830574a030

13 years agoadd 313 sample
Don Armstrong [Thu, 5 Jan 2006 06:05:12 +0000 (06:05 +0000)]
add 313 sample

git-svn-id: file:///srv/svn/function2gene/trunk@1 a0738b58-4706-0410-8799-fb830574a030