8f030ca5d3d1ff1983acb8bcb0ea1de7fe56e3a5
hiram
Fri Sep 11 16:06:50 2026 -0700
correctly lead users to download or generate GC data from bigWigs or 2bits refs #38290
diff --git src/hg/utils/automation/asmHubGc5Percent.pl src/hg/utils/automation/asmHubGc5Percent.pl
index 451b7d35b27..31d3b59b068 100755
--- src/hg/utils/automation/asmHubGc5Percent.pl
+++ src/hg/utils/automation/asmHubGc5Percent.pl
@@ -1,83 +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";
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 = "";
my $noEm = "";
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);
-if ( $gcOnFly ) {
- my $asmIdPath = &AsmHub::asmIdToPath($asmId);
- my $twoBitUrl = "https://hgdownload.soe.ucsc.edu/hubs/$asmIdPath/$accession/$accession.2bit";
- printf "
Data Access
\n";
- printf "This track is generated on-the-fly by the browser as needed.\n";
- printf "There is no existing data file for this track. To obtain the data for this track\n";
- printf "use the following kent command line program hgGcPercent:
\n";
-
- printf "hgGcPercent -wigOut -doGaps -file=stdout -win=5 -verbose=0 test \\
%s | gzip -c > %s.varStep.gz\n", $twoBitUrl, $accession;
-}
-
print <<_EOF_
Description
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.
This track may be configured in a variety of ways to highlight different
aspects of the displayed information. Click the
"Graph configuration help" link for an explanation of the
configuration options.
+
Data Access
+_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_
+This track is generated on-the-fly 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 bigWig file:
+
+ $bwUrl
+
+
+You can extract the data from that file with the
+kent command line program: bigWigToWig:
+
+
+bigWigToWig $bwUrl stdout \\
| gzip -c > $accession.gcOnFly.varStep.gz
+
+
+That bigWig data was calculated with the hgGcPercent command
+with the window size of -win=50000.
+
+To obtain the traditional 5-base window data for this track
+use the following kent command line program hgGcPercent:
+
+
+hgGcPercent -wigOut -doGaps -file=stdout -win=5 -verbose=0 test \\
$twoBitUrl \\
| gzip -c > ${accession}.varStep.gz
+
+_EOF_
+ ;
+} else {
+ my $bwUrl = "$hgDownload/hubs/$asmIdPath/$accession/bbi/$asmId.gc5Base.bw";
+print <<_EOF_
+This track is displayed from the bigWig file:
+
+
+ $bwUrl
+
+
+You can extract the data from that file with the
+kent command line program: bigWigToWig:
+
+
+bigWigToWig $bwUrl stdout \\
| gzip -c > $accession.gc5Base.varStep.gz
+
+
+Or, you can calculate that data locally at the 5-base window size
+with the following kent command line program hgGcPercent:
+
+
+hgGcPercent -wigOut -doGaps -file=stdout -win=5 -verbose=0 test \\
$twoBitUrl \\
| gzip -c > ${accession}.varStep.gz
+
+_EOF_
+ ;
+}
+print <<_EOF_
Credits
The data and presentation of this graph were prepared by
Hiram Clawson.
_EOF_
;