Commits for angie

v244_preview2 to v244_base (2010-11-30 to 2010-12-07) v244

• Track #1684 (SNPs 132 (dbSNP)): work in progress: while waiting fordbSNP to re-dump allele frequencies, I'm automating the dbSNP process (doDbSnp.pl) and using equCab2 as a nice simple non-human test case. (I would use a higher-prio species but their dump files are out of date...) doDbSnp.pl doesn't run all the way through but I'm checking it in on a branch to save the work done so far.
  • src/hg/makeDb/doc/equCab2.txt - lines changed 42, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg19.txt - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/automation/doDbSnp.pl - lines changed 1028, context: html, text, full: html, text
• Some small fixes to doDbSnp.pl to get it to run a bit farther.Currently dies when hgLoadSqlTab complains about mysql warnings, of which there are a zillion with dbSNP's dump files that have empty values in numeric columns.
  • src/hg/utils/automation/doDbSnp.pl - lines changed 15, context: html, text, full: html, text
• For some species (e.g. horse), dbSNP has absolutely no validationinfo, so in snpNNN.sql, the valid column is a set containing only 'unknown'. In that case, we need not to include a comma after 'unknown' or mysql barfs.
  • src/hg/snp/snpLoad/snpNcbiToUcsc.c - lines changed 4, context: html, text, full: html, text
• doDbSnp.pl now runs successfully on equCab2 snp130. It still needsmore consistency checks, more info and guidance for the developer upon completion, and to add the new columns (allele freq + N, clinical bit, list of submitter handles.
  • src/hg/makeDb/doc/equCab2.txt - lines changed 12, context: html, text, full: html, text
  • src/hg/utils/automation/doDbSnp.pl - lines changed 92, context: html, text, full: html, text