Commits for cline

v246_base to v247_preview (2011-01-25 to 2011-02-01) v247

• Addressing Katrina's code review feedback
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 19, context: html, text, full: html, text
• Changing the genders of several cell lines, in response to feedback from Terry Furey at Duke via Tim
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 10, context: html, text, full: html, text
• Updated the validation documents for a slew of Myers lab antibodies
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 19, context: html, text, full: html, text
• Merge branch 'master' of hgwdev.cse.ucsc.edu:/data/git/kent
• Added a stub cell growth 'protocol' for the prostate tissue. There was no cell growth protocol previously because no cells were grown: the RNA was purchased from a vendor. But, we need to have a protocol in place for the GEO submissions.
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 1, context: html, text, full: html, text
• Updated the validation types of several Myers lab antibodies
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 23, context: html, text, full: html, text
• Merge branch 'master' of cline@hgwdev.cse.ucsc.edu:/data/git/kent
• Set the genders of several cell lines to Both, following word from Terry Furey that these cell lines consist of a mixture of both male and female cells
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 8, context: html, text, full: html, text
• Merge branch 'master' of cline@hgwdev.cse.ucsc.edu:/data/git/kent
• Renamed compareRandomSample.py to checkRandomLinesExist.py, at Jim's suggestion. Merging in some minor changes to ucscGenes.
  • python/ucscgenomics/rafile/radict.pyc - lines changed 0, context: html, text, full: html, text
  • src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh - lines changed 7, context: html, text, full: html, text
  • src/hg/txGene/txGeneValidation/checkRandomLinesExist.py - lines changed 40, context: html, text, full: html, text
  • src/hg/txGene/txGeneValidation/compareRandomSample.py - lines changed 40, context: html, text, full: html, text
• At Jim's suggestion, revised mostOverlappingBed so that if there is a bed of compatible gene structure, it will be chosen, but if there isn't such a bed, then some bed will still be chosen
  • src/hg/near/hgMapToGene/hgMapToGene.c - lines changed 11, context: html, text, full: html, text
• Revised the makefile to play more nicely by copying the scripts to the directory, and removing its scripts from that directory prior to copying
  • src/hg/txGene/txGeneValidation/makefile - lines changed 6, context: html, text, full: html, text
• Merge branch 'master' of cline@hgwdev.cse.ucsc.edu:/data/git/kent
• Made the grep commands in this script prepared for some regular expression characters
  • src/hg/txGene/txGeneValidation/checkRandomLinesExist.py - lines changed 8, context: html, text, full: html, text
• Merge branch 'master' of cline@hgwdev.cse.ucsc.edu:/data/git/kent
• Removed an extraneous diagnostic statement, and abandoned the idea of escaping special characters. The calling program is responsible for taking care of grep special characters
  • src/hg/txGene/txGeneValidation/checkRandomLinesExist.py - lines changed 2, context: html, text, full: html, text
• Added a bit more testing, revised the access of the exoniphy table to account for the fact that it no longer has a numeric ID. Fortunately, it doesn't look like that ID was used for anything
  • src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes13.csh - lines changed 23, context: html, text, full: html, text
• Copying a bunch of changes from alpha to beta
  • src/hg/makeDb/trackDb/cv/beta/cv.ra - lines changed 192, context: html, text, full: html, text