kiran
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7671502e1b
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Changes from James Pirruccello: now can handle differences between UCSC and NCBI tables, properly sorting despite the contig prefix differences (presence or absence of 'chr'), and converts NCBI format to UCSC format for use by the GenomicAnnotator.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4132 348d0f76-0448-11de-a6fe-93d51630548a
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2010-08-26 19:02:29 +00:00 |
weisburd
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e7939f7036
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Fixed error message
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3653 348d0f76-0448-11de-a6fe-93d51630548a
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2010-06-28 14:50:28 +00:00 |
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weisburd
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1cb8f51f8c
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Fixed -t arg
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3634 348d0f76-0448-11de-a6fe-93d51630548a
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2010-06-24 23:44:10 +00:00 |
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weisburd
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3cd0570c1e
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Now can run with multiple processes, multiple threads, or both
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3633 348d0f76-0448-11de-a6fe-93d51630548a
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2010-06-24 23:25:01 +00:00 |
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weisburd
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dae3ce2c0f
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changed log dir
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3632 348d0f76-0448-11de-a6fe-93d51630548a
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2010-06-24 23:08:13 +00:00 |
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weisburd
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fea8054e9e
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Updated long name for -l to --run-locally
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3631 348d0f76-0448-11de-a6fe-93d51630548a
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2010-06-24 22:26:45 +00:00 |
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weisburd
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72e669538e
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Updated arg description for -s
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3629 348d0f76-0448-11de-a6fe-93d51630548a
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2010-06-24 22:04:01 +00:00 |
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weisburd
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cef12b45e1
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Fixed typo
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3561 348d0f76-0448-11de-a6fe-93d51630548a
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2010-06-15 21:17:14 +00:00 |
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weisburd
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c0370f4d0a
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Added both inclusive and exclusive filters
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3538 348d0f76-0448-11de-a6fe-93d51630548a
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2010-06-11 18:40:41 +00:00 |
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weisburd
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d1a4c4f0d3
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Added -w filter option allowing user to specify chromosomes to be skipped.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3531 348d0f76-0448-11de-a6fe-93d51630548a
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2010-06-10 20:58:25 +00:00 |
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weisburd
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6fd2d39a7d
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Modified run_locally mode to use os.system(..) instead of popen
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3515 348d0f76-0448-11de-a6fe-93d51630548a
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2010-06-09 17:10:03 +00:00 |
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weisburd
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a3ccf49f5b
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Write error to stderr
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3514 348d0f76-0448-11de-a6fe-93d51630548a
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2010-06-09 17:09:10 +00:00 |
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weisburd
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2b31975cb4
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Added more options for coordinate systems - now you can add 1 to either the start coordinates, the end coordinates, or both
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3508 348d0f76-0448-11de-a6fe-93d51630548a
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2010-06-08 22:49:19 +00:00 |
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weisburd
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410afcdf2c
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Added parallelization options - when running locally, multiple processes can be spawned, or a -nt arg can be specified to run each TranscriptToInfo instance multi-threaded
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3507 348d0f76-0448-11de-a6fe-93d51630548a
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2010-06-08 22:48:07 +00:00 |
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weisburd
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92c72d3361
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Added back lines that update the *big-table-header.txt file before using it
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3506 348d0f76-0448-11de-a6fe-93d51630548a
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2010-06-08 22:45:41 +00:00 |
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weisburd
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3c24223d02
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Script for concatenating 2 AnnotatorInputTables, and writing the result to standard out. Merge-sorts the 2 tables while concatenating them
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3505 348d0f76-0448-11de-a6fe-93d51630548a
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2010-06-08 22:44:16 +00:00 |
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weisburd
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04e14ef85a
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Refactored so it could be used for knownGene and CCDS as well as refGene
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3373 348d0f76-0448-11de-a6fe-93d51630548a
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2010-05-18 02:45:11 +00:00 |
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weisburd
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f120a00433
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Fixed bug so that the strand, alternate, and reference columns are now moved correctly
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3342 348d0f76-0448-11de-a6fe-93d51630548a
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2010-05-10 17:59:39 +00:00 |
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weisburd
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a462b5e1e7
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Changed a default path
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3291 348d0f76-0448-11de-a6fe-93d51630548a
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2010-05-03 17:07:21 +00:00 |
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weisburd
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28f746b76a
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Added option to generate UCSC or NCBI sequence
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3283 348d0f76-0448-11de-a6fe-93d51630548a
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2010-04-30 17:26:00 +00:00 |
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weisburd
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c214056d88
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Script for concatenating results of GenerateTranscriptToInfo.py into one big file
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3279 348d0f76-0448-11de-a6fe-93d51630548a
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2010-04-30 15:47:08 +00:00 |
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weisburd
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0069cb426d
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Script for spawning LSF jobs that run the TranscriptToInfo.java walker on each of the 50 contigs.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3277 348d0f76-0448-11de-a6fe-93d51630548a
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2010-04-30 15:27:52 +00:00 |
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weisburd
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ba7fe7c4e1
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Renamed
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3276 348d0f76-0448-11de-a6fe-93d51630548a
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2010-04-30 15:25:07 +00:00 |
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weisburd
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4937295a0b
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Renamed
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3275 348d0f76-0448-11de-a6fe-93d51630548a
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2010-04-30 15:24:56 +00:00 |
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weisburd
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c7b4f78316
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Added -m arg
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3233 348d0f76-0448-11de-a6fe-93d51630548a
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2010-04-21 22:38:47 +00:00 |
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weisburd
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04c22a6640
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Added handling of UCSC and NCBI reference sequences
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3165 348d0f76-0448-11de-a6fe-93d51630548a
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2010-04-14 14:40:31 +00:00 |
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weisburd
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2183f10a1d
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Script for validating and converting text files into the tabular format required for GenomicAnnotator -B inputs
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3156 348d0f76-0448-11de-a6fe-93d51630548a
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2010-04-13 13:35:10 +00:00 |