cf078156da3eb0042503c279d0c0bddb9786c355
hiram
  Thu Mar 5 12:01:59 2020 -0800
now running up Ensembl genes on assembly hubs refs #24963

diff --git src/hg/utils/automation/asmHubEnsGene.pl src/hg/utils/automation/asmHubEnsGene.pl
index 4a4b82a..d8f08cf 100755
--- src/hg/utils/automation/asmHubEnsGene.pl
+++ src/hg/utils/automation/asmHubEnsGene.pl
@@ -1,85 +1,105 @@
 #!/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 != 4) {
   printf STDERR "usage: asmHubEnsGene.pl asmId asmId.names.tab bbi/asmId ensVersion\n";
   printf STDERR "where asmId is the assembly identifier,\n";
   printf STDERR "and   asmId.names.tab is naming file for this assembly,\n";
   printf STDERR "and bbi/asmId is the path prefix to .ensGene.bb.\n";
   printf STDERR "the ensVersion is from trackData/ensGene/version.txt\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
+}
+
+# $scriptDir/asmHubEnsGene.pl $asmId $buildDir/html/$asmId.names.tab $buildDir/bbi/$asmId > $buildDir/html/$asmId.ensGene.html "${ensVersion}"
+
 my $asmId = shift;
 my $namesFile = shift;
 my $bbiPrefix = shift;
 my $ensVersion = shift;
 my $ensGeneBbi = "$bbiPrefix.ensGene.bb";
+my $runDir = $bbiPrefix;
+$runDir =~ s#/bbi/.*#/trackData/ensGene#;
+my $fbResults = "${runDir}/fb.$asmId.ensGene.txt";
+my $fbBases = "";
+if ( -s "${fbResults}" ) {
+  ($fbBases, undef) = split('\s+', `cat $fbResults`);
+}
 
 if ( ! -s $ensGeneBbi ) {
   printf STDERR "ERROR: can not find ensGene bbi file:\n\t'%s'\n", $ensGeneBbi;
   exit 255;
 }
 
 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;
 my $geneCount = `bigBedInfo $ensGeneBbi | egrep "itemCount:|basesCovered:" | xargs echo | sed -e 's/itemCount/Gene count/; s/ basesCovered/; Bases covered/;'`;
 chomp $geneCount;
+if (length($fbBases)) {
+  $geneCount .= sprintf(" (%s bases in exons only)", commify($fbBases));
+}
 
 print <<_EOF_
 <h2>Description</h2>
 <p>
 This track shows the Ensembl gene, $ensVersion, annotations on
 the $assemblyDate $em${organism}$noEm/$asmId genome assembly.<br>
 <br>
 These gene predictions were generated by
 <a href="http://www.ensembl.org/index.html" target="_blank">Ensembl</a>.<br>
 <br>
 $geneCount
 </p>
 
 <h2>Methods</h2>
 
 <p>
 For a description of the methods used in Ensembl gene predictions, please
 refer to
 <a href="https://academic.oup.com/nar/article/30/1/38/1332872/The-Ensembl-genome-database-project"
 target="_blank">Hubbard <em>et al</em>. (2002)</a>,
 also listed in the References section below.
 </p>
 
 <h2>Credits</h2>
 
 <p>
 We would like to thank Ensembl for providing this annotation.  For more information, please see:
 <a href="http://www.ensembl.org/info/genome/genebuild/genome_annotation.html" target=_blank>Ensembl&#39;s genome annotation page.</a>
 </p>
 
 <h2>References</h2>
 
 <p>
 Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J,
 Curwen V, Down T <em>et al</em>.
 <a href="https://academic.oup.com/nar/article/30/1/38/1332872/The-Ensembl-genome-database-project"
 target="_blank">The Ensembl genome database project</a>.
 <em>Nucleic Acids Res</em>. 2002 Jan 1;30(1):38-41.
 PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11752248" target="_blank">11752248</a>; PMC: <a
 href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC99161/" target="_blank">PMC99161</a>
 </p>
 _EOF_
    ;