f654134d5172e2687b3e6f98da7db78dd8379387
hiram
  Tue Jan 21 15:01:57 2020 -0800
initial set of files to build "other vertebrates" assembly hub refs #2482

diff --git src/hg/makeDb/doc/vertebratesAsmHub/mkGenomes.pl src/hg/makeDb/doc/vertebratesAsmHub/mkGenomes.pl
new file mode 100755
index 0000000..ad51cf0
--- /dev/null
+++ src/hg/makeDb/doc/vertebratesAsmHub/mkGenomes.pl
@@ -0,0 +1,182 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+use File::Basename;
+
+my %betterName;	# key is asmId, value is common name
+my $hubName = "vertebrate";
+my $srcDocDir = "vertebratesAsmHub";
+my $buildDir = "/hive/data/genomes/asmHubs/refseqBuild";
+my $destDir = "/hive/data/genomes/asmHubs/$hubName";
+
+my $home = $ENV{'HOME'};
+my $srcDir = "$home/kent/src/hg/makeDb/doc/$srcDocDir";
+my $commonNameList = "$hubName.asmId.commonName.tsv";
+my $commonNameOrder = "$hubName.commonName.asmId.orderList.tsv";
+
+
+open (FH, "<$srcDir/${commonNameList}") or die "can not read $srcDir/${commonNameList}";
+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 $assemblyCount = 0;
+
+open (FH, "<$srcDir/${commonNameOrder}") or die "can not read ${commonNameOrder}";
+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 $buildDir = "/hive/data/genomes/asmHubs/refseqBuild/" . substr($asmId, 0 ,3);
+  $buildDir .= "/" . substr($asmId, 4 ,3);
+  $buildDir .= "/" . substr($asmId, 7 ,3);
+  $buildDir .= "/" . substr($asmId, 10 ,3);
+  $buildDir .= "/" . $asmId;
+  my $asmReport="$buildDir/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 $buildDir/$asmId.chrom.sizes | awk '{print \$1}'`;
+  chomp $chrName;
+  my $bigChrom=`head -1 $buildDir/$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 $localGenomesFile = "$buildDir/${asmId}.genomes.txt";
+  open (GF, ">$localGenomesFile") or die "can not write to $localGenomesFile";
+  printf GF "genome %s\n", $asmId;
+  printf GF "trackDb %s.trackDb.txt\n", $asmId;
+  printf GF "groups %s.groups.txt\n", $asmId;
+  printf GF "description %s\n", $orgName;
+  printf GF "twoBitPath %s.2bit\n", $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 html/%s.description.html\n", $asmId;
+  close (GF);
+  my $localHubTxt = "$buildDir/${asmId}.hub.txt";
+  open (HT, ">$localHubTxt") or die "can not write to $localHubTxt";
+  printf HT "hub %s genome assembly\n", $asmId;
+  printf HT "shortLabel %s\n", $orgName;
+  printf HT "longLabel %s/%s/%s genome assembly\n", $orgName, $descr, $asmId;
+  printf HT "genomesFile %s.genomes.txt\n", $asmId;
+  printf HT "email hclawson\@ucsc.edu\n";
+  printf HT "descriptionUrl html/%s.description.html\n", $asmId;
+  close (HT);
+
+  my $localGroups = "$buildDir/${asmId}.groups.txt";
+  open (GR, ">$localGroups") or die "can not write to $localGroups";
+  print GR <<_EOF_
+name user
+label Custom
+priority 1
+defaultIsClosed 1
+
+name map
+label Mapping
+priority 2
+defaultIsClosed 0
+
+name genes
+label Genes
+priority 3
+defaultIsClosed 0
+
+name rna
+label mRNA
+priority 4
+defaultIsClosed 0
+
+name regulation
+label Regulation
+priority 5
+defaultIsClosed 0
+
+name compGeno
+label Comparative
+priority 6
+defaultIsClosed 0
+
+name varRep
+label Variation
+priority 7
+defaultIsClosed 0
+
+name x
+label Experimental
+priority 10
+defaultIsClosed 1
+_EOF_
+   ;
+   close (GR);
+}
+
+__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
+