 Greg Von Kuster
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05df900b3d
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Metadata will now be set on all output datasets when getting encode data.
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2008-01-03 14:12:07 +00:00 |
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Greg Von Kuster
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637c9f02c4
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Fixes for random intervals tool.
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2008-01-02 21:40:59 +00:00 |
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Greg Von Kuster
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be91b8eed0
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Better error handling for gencode_partition tool, also added functional test for the tool.
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2008-01-02 14:47:30 +00:00 |
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Greg Von Kuster
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75b84e0e4d
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Eliminated Dataset.state.FAKE (requires db update), replacing it with Dataset.state.OK since fake datasets are removed, causing problems for workflow.
Database update:
update dataset set state = 'ok' where state = 'fake'
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2007-12-21 19:31:58 +00:00 |
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Greg Von Kuster
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e94d18ad63
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A better way to decompress UCSC gzipped files. Added functional tests for uploading binary, zipped and gzipped files. Added temp file removal to upload when exception thrown. Eliminated an unnecessary import in subtract_query.
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2007-12-20 18:49:03 +00:00 |
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Greg Von Kuster
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c9b5c52cc4
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Fix for get_flanks when negative value is entered for length.
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2007-12-20 15:57:23 +00:00 |
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Greg Von Kuster
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73507a1aa3
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Fix for reading gzipped data from UCSC larger than 1 Mb in size.
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2007-12-20 14:47:11 +00:00 |
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Greg Von Kuster
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e54be223b2
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Better way to skip invalid comment lines in filtering tool. Better numerical value checks in interval.py.
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2007-12-18 14:52:04 +00:00 |
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Chinmay Rao
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7a366bcec4
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Committing EMBOSS v5.0 tools tcode textsearch tmap twofeat vectorstrip wordmatch with associated functional test files
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2007-12-17 14:38:16 +00:00 |
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Chinmay Rao
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f955d77ec3
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Adding EMBOSS v5.0 tools seqret showfeat shuffleseq sigcleave sixpack skipseq supermatcher syco
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2007-12-17 14:35:58 +00:00 |
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Chinmay Rao
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1843e0034c
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Adding EMBOSS v5.0 newcpgreport noreturn patmatdb pepinfo pepnet pepwheel pepwindow pepwindowall plotcon pepcoil pepstats plotorf polydot noreturn octanol oddcomp
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2007-12-17 14:26:48 +00:00 |
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Chinmay Rao
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9cbcae2402
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Committing EMBOSS v5.0 tools marscan maskfeat maskseq matcher megamerger merger and associated test files.
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2007-12-17 14:16:37 +00:00 |
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Chinmay Rao
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3b4bfb49c0
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Adding EMBOSS tools version 5.0 for helixturnhelix, hmoment, iep infoseq lindna and associated test files
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2007-12-17 14:10:03 +00:00 |
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Chinmay Rao
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87ce8bd4b4
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Committing EMBOSS v5 tools: epestfind, est2genome extractseq freak fuzzpro garnier geecee
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2007-12-17 14:02:48 +00:00 |
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Chinmay Rao
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d009d08342
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Adding EMBOSS v5 tools coderet cpgplot diffseq digest dotmatcher dotpath dottup dreg and associated wrapper files
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2007-12-17 13:58:30 +00:00 |
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Greg Von Kuster
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737bdf23f9
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Enhanced upload to handle certain binary and zip files. Cleaned up the upload config. Added 4 new data types: ab1, scf, binseq.zip and txtseq.zip. Added Regional Variation section to tool_conf.xml.main.
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2007-12-14 21:07:11 +00:00 |
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Greg Von Kuster
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58afe0f9ce
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Cleaned up error handling, added exception handling in ucsc_tablebrowser.py
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2007-12-13 15:01:45 +00:00 |
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Chinmay Rao
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c2c4cf84b4
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EMBOSS Version 5 for primersearch revseq seqmatchall sirna splitter tranalign transeq
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2007-12-12 22:56:38 +00:00 |
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Chinmay Rao
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4421fce049
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Upgrading EMBOSS tools to version 5.0 - trimest trimseq wobble union water wordcount prettyseq pasteseq
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2007-12-12 22:27:21 +00:00 |
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Greg Von Kuster
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a6cb37aa79
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A fix for the UCSCOutWrapper class resulting in a better exception handler for wiggle_to_simple.
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2007-12-12 20:01:26 +00:00 |
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Greg Von Kuster
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7718b28839
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Better error condition handling for some tools. I've made these changes because anything printed to stderr now results in the tool state being "error" and tools with this state are no longer allowed as input datasets for tools.
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2007-12-12 19:30:26 +00:00 |
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Greg Von Kuster
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02ef201032
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Added exception handling to wiggle_to_simple.
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2007-12-12 18:15:22 +00:00 |
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Chinmay Rao
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19c4601e90
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Adding version 5.0 of EMBOSS tools dan degapseq descseq codcmp and palindrome
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2007-12-12 16:38:36 +00:00 |
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Chinmay Rao
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4d6a115f74
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Upgrading EMBOSS tools newseq notseq nthseq to version 5.0
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2007-12-11 23:25:49 +00:00 |
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Greg Von Kuster
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4fda68c476
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Bug fix in histogram tool.
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2007-12-11 21:41:31 +00:00 |
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Chinmay Rao
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5f4ea17fd8
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EMBOSS tools upgrade to version 5.0 - msbar, needle and newcpgseek
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2007-12-11 21:17:10 +00:00 |
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Chinmay Rao
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73e52be7a0
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Version 5.0 for EMBOSS tools fuzztran, getorf and isochore
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2007-12-11 21:01:52 +00:00 |
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Greg Von Kuster
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d61ae1181e
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Bug fix in biomart - metadata will now be correctly set for biomart data.
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2007-12-11 18:40:30 +00:00 |
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Chinmay Rao
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54aa1bf33e
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Upgrading EMBOSS tools equicktandem, etandem and fuzznuc to version 5.0
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2007-12-11 17:17:49 +00:00 |
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Chinmay Rao
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871405c515
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Version 5.0 of EMBOSS tools cusp cutseq einverted.
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2007-12-11 17:01:26 +00:00 |
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Chinmay Rao
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577cf1218a
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Upgrading EMBOSS tools cirdna compseq and cpgreport to Version 5.0
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2007-12-11 16:50:49 +00:00 |
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Chinmay Rao
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bfa11001ce
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Upgrading EMBOSS tools charge, checktrans and chips to version 5.0
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2007-12-11 16:40:58 +00:00 |
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Chinmay Rao
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c5aa37fd91
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Upgrading EMBOSS tools btwsited, cai, custom cai and chaos to version 5.0
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2007-12-11 16:31:09 +00:00 |
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Chinmay Rao
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670d0adec2
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2007-12-11 16:19:53 +00:00 |
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Chinmay Rao
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3539fb038d
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Version 5.0 of EMBOSS Antigenic tool.
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2007-12-11 15:59:01 +00:00 |
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Greg Von Kuster
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f7f7aeab26
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Fixed a security flaw in upload.py. Added a unit test for get_file_peek() to data.py, along with outher cleanup. Corrected gbrowse display links in interval.py. Bug fixes in root.py where google bots were throwing exceptions.
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2007-12-10 21:00:21 +00:00 |
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Greg Von Kuster
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bbba08b89d
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Gzipped files from UCSC will now be decompressed on the fly. Also fixed a bug in biomart_filter.
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2007-12-10 16:13:05 +00:00 |
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Greg Von Kuster
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ab1d867915
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More dynamic options cleanup. Eliminated the "tool_type" attribute, among other cleanup chores.
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2007-11-30 20:08:21 +00:00 |
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Greg Von Kuster
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396ca8c43e
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Uncommented functional tests in some regVariation tools in preparation for moving them to main.
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2007-11-30 13:43:59 +00:00 |
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Greg Von Kuster
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87c0138d6d
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Fixed bug I introduced in quality_filter.xml
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2007-11-29 21:25:11 +00:00 |
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Daniel Blankenberg
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9efcb80fe3
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More MAF tools now have better behavior when no species are selected.
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2007-11-29 18:13:48 +00:00 |
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Greg Von Kuster
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79745f4012
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Modified all tools to use the new <options> tag for dynamic select lists. Completely eliminated the <select_options> tag approach. With the exception of find_clusters_mysql, the old dynamic_options approach is not being used by any tool, although dynamic_options is still supported in parameters.py.
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2007-11-29 17:04:42 +00:00 |
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Guruprasad Anada
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ab85984841
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Adding tool "Get Indel rates for 3-way alignments" under Regional variation section.
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2007-11-28 18:56:13 +00:00 |
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Daniel Blankenberg
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83d2926577
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Enhance interval_maf stitching tool to work when no species are selected ==> defaults to providing all species available.
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2007-11-28 18:12:03 +00:00 |
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Guruprasad Anada
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71979fb76f
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Added Feature coverage tool under Regional variation section. Also, cleaned up regVariation folder.
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2007-11-26 15:36:33 +00:00 |
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Greg Von Kuster
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300d66fb11
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Modified tools using the <select_options> tag approach for dynamic options to use the new <select> tag approach. I modified the microbial import tool to use the older <select_options> approach last week and will modify it to use the new <select> approach next week. A few tools still use the oldest dynamic_options attribute approach, but modifying them to use the new <select> tag will be trivial. I'll do this when I return.
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2007-11-21 18:48:37 +00:00 |
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Guruprasad Anada
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b52524892e
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Regional variation tools: Tool xmls, code files and test-data added for 4 regional variation tools.
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2007-11-19 21:55:45 +00:00 |
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Greg Von Kuster
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71d16671bc
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First pass at final phase of cleaning up approach to dynamic select lists. Added a functional test to phastOdds tool. The following tools now use this latest approach to dynamic optioons:
axt_to_fasta, phastOdds, axt_to_lav, random_intervals, extractAxt_wrapper, axt_to_concat_fasta, aggregate_binned_scores.
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2007-11-16 20:08:31 +00:00 |
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Daniel Blankenberg
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0e9c5bdbd9
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Minor update to interval2maf.py display of error messages.
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2007-11-16 17:39:49 +00:00 |
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Daniel Blankenberg
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48d718bca6
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Fix comparison of file contents for test framework. It was previously using zip(), so tests would wrongly pass when one file was smaller than the other (but contained the same data up to it's end).
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2007-11-14 22:00:29 +00:00 |
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