pchan: changes by commit

branch to review (2010-02-16 to 2010-02-23) v226

• create script to get metagenome info and sequences, initially from JGI IMG/M
  • src/hg/archaeStuff/scripts/make-metagenome-info 1.1 - lines changed: 760, context: html, text, full: html, text
• fix problem when org name has slashes
  • src/hg/archaeStuff/scripts/make-metagenome-info 1.2 - lines changed: 1, context: html, text, full: html, text
• add multiz for Synechococcus
  • src/hg/archaeStuff/data/Genome-info-mods 1.98 - lines changed: 8, context: html, text, full: html, text
• fix tracksDb dir in multiz creation
  • src/hg/archaeStuff/scripts/archaeBrowser/MultiAlignment.pm 1.11 - lines changed: 1, context: html, text, full: html, text
• add Private in Tax_ID for all private metagenomes
  • src/hg/archaeStuff/data/Genome-info-meta 1.13 - lines changed: 11, context: html, text, full: html, text
• add code to support IMG metagenome loading
  • src/hg/archaeStuff/scripts/archaeBrowser/CDS.pm 1.25 - lines changed: 108, context: html, text, full: html, text
  • src/hg/archaeStuff/scripts/archaeBrowser/Constant.pm 1.41 - lines changed: 1, context: html, text, full: html, text
  • src/hg/archaeStuff/scripts/archaeBrowser/GenomeInfo.pm 1.18 - lines changed: 12, context: html, text, full: html, text
  • src/hg/archaeStuff/scripts/archaeBrowser/Organism.pm 1.11 - lines changed: 16, context: html, text, full: html, text
  • src/hg/archaeStuff/scripts/archaeBrowser/OrganismDb.pm 1.51 - lines changed: 58, context: html, text, full: html, text
  • src/hg/archaeStuff/scripts/archaeBrowser/ncRNA.pm 1.23 - lines changed: 79, context: html, text, full: html, text
• fix bug in formatting locus tag for IMG metagenome
  • src/hg/archaeStuff/scripts/archaeBrowser/CDS.pm 1.26 - lines changed: 1, context: html, text, full: html, text
  • src/hg/archaeStuff/scripts/archaeBrowser/ncRNA.pm 1.24 - lines changed: 1, context: html, text, full: html, text
  • src/hg/archaeStuff/scripts/make-metagenome-info 1.3 - lines changed: 1, context: html, text, full: html, text
• fix locus tag for metagenomes when not exists in IMG
  • src/hg/archaeStuff/scripts/archaeBrowser/CDS.pm 1.27 - lines changed: 1, context: html, text, full: html, text
  • src/hg/archaeStuff/scripts/archaeBrowser/ncRNA.pm 1.25 - lines changed: 1, context: html, text, full: html, text
  • src/hg/archaeStuff/scripts/make-metagenome-info 1.4 - lines changed: 2, context: html, text, full: html, text
• Use publication instead of isolation for metagenomes
  • src/hg/archaeStuff/scripts/archaeBrowser/OrganismDb.pm 1.52 - lines changed: 9, context: html, text, full: html, text
• remove GOLD ID line if value does not exist
  • src/hg/archaeStuff/scripts/archaeBrowser/OrganismDb.pm 1.53 - lines changed: 4, context: html, text, full: html, text
• add multiz for IMG cistern spring, joseph coats, and monarch geyser
  • src/hg/archaeStuff/data/Genome-info-meta 1.14 - lines changed: 12, context: html, text, full: html, text