Commits for cline

v256_preview to v256_preview2 (2011-08-16 to 2011-08-23) v256

• It turns out that there were several cases of duplicate tags, i.e. two distinct stanzas with the same tag, and the validator wasn't catching this. Just resolved the duplicate tags
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 12, context: html, text, full: html, text
• (1) Removed a comment indicating that two cell lines have the same tag, when this problem was fixed last week and the two cell lines no longer have the same tag. (2) Accepted several provisional view stanzas. (3) Accepted a provisional change on the t-rex cell line
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 10, context: html, text, full: html, text
• Copied cvMaven branch changes into the beta cvQA branch on beta. What should be different is that some tags have been modified so that all tags are unique
  • src/hg/makeDb/trackDb/cv/beta/cv.ra - lines changed 74, context: html, text, full: html, text
• Added the proteogenomics supertrack
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSuper.ra - lines changed 7, context: html, text, full: html, text
• To address Redmine issue #411, created two new tables knownGeneTxMrna and knownGeneTxPep. These files contain respectively the mRNA sequence that would be produced by transcribing the exons in each UCSC Gene gene prediction, and translating those sequences. They differ from knownGeneMrna and knownGenePep in that those files contain copies of the RefSeq mRNA and RefPep protein for transcripts that are derived from RefSeq. These are verbatim copies of the sequence, including regions that don't align to the genome. This has led to confusion, including TCGA losing a fair bit of time in a mis-assumption that these sequences were direct transcripts of the gene predictions. So, to address the issue, we're adding direct transcripts of the gene predictions, and (still) looking for the appropriate place to document which sequences are which
  • src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh - lines changed 9, context: html, text, full: html, text
  • src/hg/txGene/txGeneProtAndRna/txGeneProtAndRna.c - lines changed 31, context: html, text, full: html, text
• Renamed the display heading as indicated by Jacob
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeProtGenoSuper.html - lines changed 1, context: html, text, full: html, text
• Initializing repProtSeq
  • src/hg/txGene/txGeneProtAndRna/txGeneProtAndRna.c - lines changed 2, context: html, text, full: html, text
• Addressing pre-QA feedback from Redmine ticket # 4944, issue # 4
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeProtGenoSuper.html - lines changed 10, context: html, text, full: html, text
• Merge branch 'cvQA'
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 4, context: html, text, full: html, text
• Accepted provisional changes
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 14, context: html, text, full: html, text
• Added amino acids U (selenocysteine), O (pyrrolysine) and J (leucine OR isoleucine)
  • src/hg/protein/pbCalDist/pbCalDist.c - lines changed 1, context: html, text, full: html, text
• Updated the proteins database referenced
  • src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh - lines changed 14, context: html, text, full: html, text
• (1) In response to loads of warning messages that U is an invalid amino acid, when actually it's not, I updated the expected amino acid alphabet in many places. I added U (selenocysteine), O (pyrrolysine) and J (a wildcard indicating either leucine or isoleucine). In many places, I replaced a hardcoded amino acid alphabet size with the strlen of the string of expected amino acids. And in one place, I replaced a hardcoded protein database name with a command line argument, and changed the UCSC Genes script accordingly
  • src/hg/protein/pbCalDist/pbCalDist.c - lines changed 3, context: html, text, full: html, text
  • src/hg/protein/pbCalDistGlobal/pbCalDistGlobal.c - lines changed 4, context: html, text, full: html, text
  • src/hg/protein/pbCalResStd/pbCalResStd.c - lines changed 14, context: html, text, full: html, text
  • src/hg/protein/pbCalResStdGlobal/pbCalResStdGlobal.c - lines changed 3, context: html, text, full: html, text
  • src/hg/protein/pbGlobal/pbGlobal.c - lines changed 1, context: html, text, full: html, text
  • src/hg/protein/pbTracks/pbTracks.c - lines changed 1, context: html, text, full: html, text
• Addressed Redmine Bug # 2712, which concerns entries in the kgXref table for which the gene symbol and the description are inconsistent. This bug occurs when the gene symbol and the description are being pulled out of the genbank records for the sequences used as evidence (i.e. when there's no RefSeq record to rely on). It happens because the gene symbol and description are derived from separate queries, which are periodically inconsistent. To resolve this, I added some logic to the code to first try to get the gene symbol AND description from GenBank records that have both; failing that, get the gene symbol, and get the GenBank record separately
  • src/hg/txGene/txGeneXref/txGeneXref.c - lines changed 40, context: html, text, full: html, text