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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
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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
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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
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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
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Don Armstrong [Thu, 14 Feb 2008 05:55:29 +0000 (05:55 +0000)]
add todo
git-svn-id: file:///srv/svn/function2gene/trunk@32
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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
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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
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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
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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
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Don Armstrong [Wed, 23 Jan 2008 01:11:39 +0000 (01:11 +0000)]
* Update readme
git-svn-id: file:///srv/svn/function2gene/trunk@27
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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
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Don Armstrong [Tue, 15 Jan 2008 00:04:14 +0000 (00:04 +0000)]
* Update readme
git-svn-id: file:///srv/svn/function2gene/trunk@25
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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