cbf5cf161c1be2f6bfdcee0a29f334564ac9435e
hiram
  Fri Sep 11 16:11:38 2026 -0700
silence claude noise refs #38290

diff --git src/hg/utils/automation/asmHubGc5Percent.pl src/hg/utils/automation/asmHubGc5Percent.pl
index 31d3b59b068..e46222c5735 100755
--- src/hg/utils/automation/asmHubGc5Percent.pl
+++ src/hg/utils/automation/asmHubGc5Percent.pl
@@ -1,137 +1,137 @@
 #!/usr/bin/env perl
 
 use strict;
 use warnings;
 use FindBin qw($Bin);
 use lib "$Bin";
 use AsmHub;
 
 my $argc = scalar(@ARGV);
 
 if ($argc != 3) {
   printf STDERR "usage: asmHubGc5Percent.pl asmId asmId.names.tab buildDir\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   buildDir is the directory with bbi/asmId.gc5Base.bw.\n";
+  printf STDERR "and   buildDir is the directory with bbi/asmId.gc5Base|gcOnFly.bw.\n";
   exit 255;
 }
 
 my $asmId = shift;
 my $namesFile = shift;
 my $buildDir = shift;
 my $hgDownload = "https://hgdownload.soe.ucsc.edu";
 my $gc5Bw = "$buildDir/bbi/$asmId.gc5Base.bw";
 my $gcOnFly = 0;
 if ( ! -s $gc5Bw ) {
   $gc5Bw = "$buildDir/bbi/$asmId.gcOnFly.bw";
   $gcOnFly = 1;
 }
 
 if ( ! -s $gc5Bw ) {
   printf STDERR "ERROR: can not find gc5Base.bw or gcOnFly.bw file:\n\t'%s'\n", $gc5Bw;
   exit 255;
 }
 
 my @accParts = split('_', $asmId);
 my $accession = "$accParts[0]_$accParts[1]";
 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 $averageGC = `/cluster/bin/x86_64/bigWigInfo $gc5Bw | egrep "mean:" | sed -e 's/mean: //;'`;
 chomp $averageGC;
 $averageGC = sprintf("%.2f", $averageGC);
 
 print <<_EOF_
 <h2>Description</h2>
 <p>
 The GC percent track shows the percentage of G (guanine) and C (cytosine) bases
 in 5-base windows on
 the $assemblyDate $em${organism}$noEm/$asmId/$ncbiAssemblyId genome assembly.
 High GC content is typically associated with gene-rich areas.  The average
 overall GC percent for the entire assembly is % $averageGC.
 </p>
 
 <p>
 This track may be configured in a variety of ways to highlight different
 aspects of the displayed information. Click the
 &quot;Graph configuration help&quot; link for an explanation of the
 configuration options.
 </p>
 
 <hr><h4>Data Access</h4>
 _EOF_
    ;
 
 my $asmIdPath = &AsmHub::asmIdToPath($asmId);
 my $twoBitUrl = "$hgDownload/hubs/$asmIdPath/$accession/$accession.2bit";
 
 if ( $gcOnFly ) {
   my $bwUrl = "$hgDownload/hubs/$asmIdPath/$accession/bbi/$asmId.gcOnFly.bw";
 print <<_EOF_
 <p>This track is generated <b>on-the-fly</b> by the browser as needed up
 to a data density of 50,000 bases per pixel display.  Greater than that display
 density and the display transitions to using the <b>bigWig</b> file:<br>
 <br>
   <b><code>$bwUrl</code></b><br>
 <br>
 
 You can extract the data from that file with the
 <a href='$hgDownload/downloads.html#utilities_downloads'
  target=_blank>kent command line</a> program: <b>bigWigToWig</b>:<br>
 
 <br>
 <b><code>bigWigToWig $bwUrl stdout \\<br>&nbsp;&nbsp;&nbsp;| gzip -c &gt; $accession.gcOnFly.varStep.gz</code></b><br>
 <br>
 
 That <b>bigWig</b> data was calculated with the <b>hgGcPercent</b> command
 with the window size of <b>-win=50000</b>.<br>
 <br>
 To obtain the traditional 5-base window  data for this track
 use the following <a href='$hgDownload/downloads.html#utilities_downloads'
  target=_blank>kent command line</a> program <b>hgGcPercent</b>:<br>
 
 <br>
 <b><code>hgGcPercent -wigOut -doGaps -file=stdout -win=5 -verbose=0 test \\<br>&nbsp;&nbsp;&nbsp;$twoBitUrl \\<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;| gzip -c &gt; ${accession}.varStep.gz</code></b>
 </p>
 _EOF_
   ;
 } else {
   my $bwUrl = "$hgDownload/hubs/$asmIdPath/$accession/bbi/$asmId.gc5Base.bw";
 print <<_EOF_
 <p>This track is displayed from the <b>bigWig</b> file:<br>
 
 <br>
    <b><code>$bwUrl</code></b><br>
 <br>
 
 You can extract the data from that file with the
 <a href='$hgDownload/downloads.html#utilities_downloads'
  target=_blank>kent command line</a> program: <b>bigWigToWig</b>:<br>
 
 <br>
 <b><code>bigWigToWig $bwUrl stdout \\<br>&nbsp;&nbsp;&nbsp;| gzip -c &gt; $accession.gc5Base.varStep.gz</code></b><br>
 <br>
 
 Or, you can calculate that data locally at the 5-base window size
 with the following <a href='$hgDownload/downloads.html#utilities_downloads'
  target=_blank>kent command line</a> program <b>hgGcPercent</b>:<br>
 <br>
 
 <b><code>hgGcPercent -wigOut -doGaps -file=stdout -win=5 -verbose=0 test \\<br>&nbsp;&nbsp;&nbsp;$twoBitUrl \\<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;| gzip -c &gt; ${accession}.varStep.gz</code></b>
 </p>
 _EOF_
   ;
 }
 print <<_EOF_
 <h2>Credits</h2>
 <p> The data and presentation of this graph were prepared by
 <a href="mailto:&#104;&#105;&#114;a&#109;&#64;&#115;&#111;&#101;
 .&#117;&#99;&#115;&#99;.&#101;&#100;u">Hiram Clawson</a>.
 </p>
 _EOF_
    ;