a6931e479d3f8415a57fb979b759537cbc6e0ab0
hiram
  Thu Aug 8 22:16:57 2019 -0700
xenoRefGene ready to go refs #23734

diff --git src/hg/utils/automation/asmHubXenoRefGene.pl src/hg/utils/automation/asmHubXenoRefGene.pl
new file mode 100755
index 0000000..ef7d554
--- /dev/null
+++ src/hg/utils/automation/asmHubXenoRefGene.pl
@@ -0,0 +1,83 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+use FindBin qw($Bin);
+use lib "$Bin";
+use AsmHub;
+use File::Basename;
+
+my $argc = scalar(@ARGV);
+
+if ($argc != 3) {
+  printf STDERR "usage: asmHubXenoRefGene.pl asmId asmId.names.tab .../trackData/\n";
+  printf STDERR "where asmId is the assembly identifier,\n";
+  printf STDERR "and .../trackData/ is the path to the /trackData/ directory.\n";
+  exit 255;
+}
+
+# from Perl Cookbook Recipe 2.17, print out large numbers with comma
+# delimiters:
+sub commify($) {
+    my $text = reverse $_[0];
+    $text =~ s/(\d\d\d)(?=\d)(?!\d*\.)/$1,/g;
+    return scalar reverse $text
+}
+
+my $asmId = shift;
+my $namesFile = shift;
+my $trackDataDir = shift;
+my $xenoRefGeneBbi = "$trackDataDir/xenoRefGene/$asmId.xenoRefGene.bb";
+my $asmType = "refseq";
+
+if ( ! -s $xenoRefGeneBbi ) {
+  printf STDERR "ERROR: can not find $asmId.xenoRefGene.bb file\n";
+  exit 255;
+}
+
+my @partNames = split('_', $asmId);
+my $ftpDirPath = sprintf("%s/%s/%s/%s/%s", $partNames[0],
+   substr($partNames[1],0,3), substr($partNames[1],3,3),
+   substr($partNames[1],6,3), $asmId);
+
+$asmType = "genbank" if ($partNames[0] =~ m/GCA/);
+my $totalBases = `ave -col=2 $trackDataDir/../${asmId}.chrom.sizes | grep "^total" | awk '{printf "%d", \$2}'`;
+chomp $totalBases;
+my $geneStats = `cat $trackDataDir/xenoRefGene/${asmId}.xenoRefGene.stats.txt | awk '{printf "%d\\n", \$2}' | xargs echo`;
+chomp $geneStats;
+my ($itemCount, $basesCovered) = split('\s+', $geneStats);
+my $percentCoverage = sprintf("%.3f", 100.0 * $basesCovered / $totalBases);
+$itemCount = commify($itemCount);
+$basesCovered = commify($basesCovered);
+$totalBases = commify($totalBases);
+
+my $em = "<em>";
+my $noEm = "</em>";
+my $assemblyDate = `grep -v "^#" $namesFile | cut -f9`;
+chomp $assemblyDate;
+my $ncbiAssemblyId = `grep -v "^#" $namesFile | cut -f10`;
+chomp $ncbiAssemblyId;
+my $organism = `grep -v "^#" $namesFile | cut -f5`;
+chomp $organism;
+
+print <<_EOF_
+<h2>Description</h2>
+<p>
+The Genbank mRNAs gene track for the $assemblyDate $em${organism}$noEm/$asmId
+genome assembly is constructed by mapping RefSeq mRNAs to this assembly
+using a blat procedure, filtered for reasonable matches.
+The mRNAs are obtained from the RefSeq release at
+<a href='ftp://ftp.ncbi.nlm.nih.gov/refseq/release/' target=_blank>
+ftp.ncbi.nlm.nih.gov/refseq/release</a>
+</p>
+
+<h2>Track statistics summary</h2>
+<p>
+<b>Total genome size: </b>$totalBases</br>
+<b>Gene count: </b>$itemCount<br>
+<b>Bases in genes: </b>$basesCovered</br>
+<b>Percent genome coverage: </b>% $percentCoverage</br>
+</p>
+
+_EOF_
+   ;