Commits for cline
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v257_base to v258_preview (2011-09-19 to 2011-09-27) v258
- Added an rfam accession field to the end of the kgXref table
- Merge branch 'kgInfoTest'
- Changed in response to Redmine #5290 (tRNA and Rfam genes being represented poorly by kgXref). The kgXref table now has two new fields: one for the tRNA name (which can be used to cross-reference the track items to tRNA Genes items), and one for the Rfam accession (which can be used for links to the appropriate Rfam model page). txGeneXref fills in both of these fields, and splices the sequence names appropriately to pull out half-meaningful gene symbols and descriptions
- src/hg/txGene/txGeneXref/txGeneXref.c - lines changed 99, context: html, text, full: html, text
- (1) Updated the genomes and files used for buidling the *BlastTabs tables. (2) fixed a bug: the fold UTR tables were being built off not the temporary database but the current database (i.e. the released version). (3) Cleaned up some scripts to run the pfam jobs with pfam on /hive/scratch, where it shouldn't have as much adverse effects on the rest of the filesystem
- src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh - lines changed 55, context: html, text, full: html, text
- Attempted to turn on score filters for this track in response to Katrina's question (#92) in Redmine Track #141. This attempt was to no avail: I still see no score filters
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.new.ra - lines changed 2, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.ra - lines changed 2, context: html, text, full: html, text
- src/hg/makeDb/trackDb/tagTypes.tab - lines changed 6, context: html, text, full: html, text
- Reviewed the databases and files to use for building the *BlastTab tables with Brooke. Revised some versions of some files to ensure that I'm building with the latest version to be released on the RR
- src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh - lines changed 10, context: html, text, full: html, text
- Updated the process of building the kegg pathway tables, modeling after what Fan did for hg19
- src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh - lines changed 37, context: html, text, full: html, text
- src/hg/rnaStructure/utrFa/utrFa.c - lines changed 13, context: html, text, full: html, text
- Revert "Updated the process of building the kegg pathway tables, modeling after what Fan did for hg19"
This reverts commit 946ad6602b09a56d6ccc661a0bfc84de9c345eac.
- src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh - lines changed 37, context: html, text, full: html, text
- src/hg/rnaStructure/utrFa/utrFa.c - lines changed 13, context: html, text, full: html, text
- Final commit of these scripts before the superuser sections get run - w00t
- src/hg/makeDb/doc/proteins/101005.txt - lines changed 12, context: html, text, full: html, text
- src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh - lines changed 9, context: html, text, full: html, text
- Replaced key declarations that had been lost when I added the tRNA and rfam fields
- Updated the knownGene track description page to reflect the changes in content
- src/hg/makeDb/trackDb/human/hg19/knownGene.html - lines changed 38, context: html, text, full: html, text
- Changed the default score filter
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.new.ra - lines changed 2, context: html, text, full: html, text
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.ra - lines changed 1, context: html, text, full: html, text
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