10a6e5cd8350a3409c7a053ac6f78be70f459c2c
hiram
  Mon Oct 7 14:20:32 2019 -0700
files to build the platinum genomes assembly hub refs #21784

diff --git src/hg/makeDb/doc/platinum/mkGenomes.pl src/hg/makeDb/doc/platinum/mkGenomes.pl
new file mode 100755
index 0000000..a63d01f
--- /dev/null
+++ src/hg/makeDb/doc/platinum/mkGenomes.pl
@@ -0,0 +1,116 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+use File::Basename;
+
+my %betterName;	# key is asmId, value is common name
+my $subDirName = "platinum";
+
+my $home = $ENV{'HOME'};
+my $srcDir = "$home/kent/src/hg/makeDb/doc/$subDirName";
+
+open (FH, "<$srcDir/commonNames.txt") or die "can not read $srcDir/commonNames.txt";
+while (my $line = <FH>) {
+  chomp $line;
+  my ($asmId, $name) = split('\t', $line);
+  $betterName{$asmId} = $name;
+}
+close (FH);
+
+my @orderList;	# asmId of the assemblies in order from the *.list files
+# the order to read the different .list files:
+my $assemblyCount = 0;
+
+open (FH, "<commonNameOrder.list") or die "can not read commonNameOrder.list";
+while (my $line = <FH>) {
+  chomp $line;
+  my ($commonName, $asmId) = split('\t', $line);
+  push @orderList, $asmId;
+  ++$assemblyCount;
+}
+close (FH);
+
+my $orderKey = 1;
+foreach my $asmId (reverse(@orderList)) {
+  my $asmReport="$asmId/download/${asmId}_assembly_report.txt";
+  my $descr=`grep -i "organism name:" $asmReport | head -1 | sed -e 's#.*organism name: *##i; s# (.*\$##;'`;
+  chomp $descr;
+  my $orgName=`grep -i "organism name:" $asmReport | head -1 | sed -e 's#.* name: .* (##; s#).*##;'`;
+  chomp $orgName;
+  $orgName = $betterName{$asmId} if (exists($betterName{$asmId}));
+
+  printf "genome %s\n", $asmId;
+  printf "trackDb genomes/%s/%s.trackDb.txt\n", $asmId, $asmId;
+  printf "groups groups.txt\n";
+  printf "description %s\n", $orgName;
+  printf "twoBitPath genomes/%s/%s.2bit\n", $asmId, $asmId;
+  printf "organism %s\n", $descr;
+  my $chrName=`head -1 $asmId/$asmId.chrom.sizes | awk '{print \$1}'`;
+  chomp $chrName;
+  my $bigChrom=`head -1 $asmId/$asmId.chrom.sizes | awk '{print \$NF}'`;
+  chomp $bigChrom;
+  my $oneThird = int($bigChrom/3);
+  my $tenK = $oneThird + 10000;
+  $tenK = $bigChrom if ($tenK > $bigChrom);
+  my $defPos="${chrName}:${oneThird}-${tenK}";
+  if ( -s "$asmId/defaultPos.txt" ) {
+    $defPos=`cat "$asmId/defaultPos.txt"`;
+    chomp $defPos;
+  }
+  printf "defaultPos %s\n", $defPos;
+  printf "orderKey %d\n", $orderKey++;
+  printf "scientificName %s\n", $descr;
+  printf "htmlPath genomes/%s/html/%s.description.html\n", $asmId, $asmId;
+  printf "\n";
+  my $localGenomesFile = "$asmId/${asmId}.genomes.txt";
+  open (GF, ">$localGenomesFile") or die "can not write to $localGenomesFile";
+  printf GF "genome %s\n", $asmId;
+  printf GF "trackDb %s/%s.trackDb.txt\n", $asmId, $asmId;
+  printf GF "groups groups.txt\n";
+  printf GF "description %s\n", $orgName;
+  printf GF "twoBitPath %s/%s.2bit\n", $asmId, $asmId;
+  printf GF "organism %s\n", $descr;
+  printf GF "defaultPos %s\n", $defPos;
+  printf GF "orderKey %d\n", $orderKey++;
+  printf GF "scientificName %s\n", $descr;
+  printf GF "htmlPath %s/html/%s.description.html\n", $asmId, $asmId;
+  close (GF);
+}
+
+__END__
+
+description Mastacembelus armatus
+twoBitPath GCA_900324485.2_fMasArm1.2/trackData/addMask/GCA_900324485.2_fMasArm1.2.masked.2bit
+organism Zig-Zag eel
+defaultPos LR535842.1:14552035-14572034
+orderKey 1
+scientificName Mastacembelus armatus
+htmlPath GCA_900324485.2_fMasArm1.2/html/GCA_900324485.2_fMasArm1.2.description.html
+
+# head -25 GCA_002180035.3_HG00514_prelim_3.0_assembly_report.txt
+
+# Assembly name:  HG00514_prelim_3.0
+# Organism name:  Homo sapiens (human)
+# Isolate:  HG00514
+# Sex:  female
+# Taxid:          9606
+# BioSample:      SAMN04229552
+# BioProject:     PRJNA300843
+# Submitter:      The Genome Institute at Washington University School of Medicine
+# Date:           2018-05-22
+# Assembly type:  haploid
+# Release type:   major
+# Assembly level: Chromosome
+# Genome representation: full
+# WGS project:    NIOH01
+# Assembly method: Falcon v. November 2016
+# Expected final version: no
+# Genome coverage: 80.0x
+# Sequencing technology: PacBio RSII
+# GenBank assembly accession: GCA_002180035.3
+#
+## Assembly-Units:
+## GenBank Unit Accession       RefSeq Unit Accession   Assembly-Unit name
+## GCA_002180045.3              Primary Assembly
+