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 @@ -7,77 +7,131 @@ 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 = "<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); -if ( $gcOnFly ) { - my $asmIdPath = &AsmHub::asmIdToPath($asmId); - my $twoBitUrl = "https://hgdownload.soe.ucsc.edu/hubs/$asmIdPath/$accession/$accession.2bit"; - printf "<hr><h4>Data Access</h4>\n"; - printf "<p>This track is generated <em>on-the-fly</em> 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 <a href='https://hgdownload.gi.ucsc.edu/downloads.html#utilities_downloads'\n"; - printf " target=_blank>kent command line</a> program <b>hgGcPercent</b>:</p>\n"; - - printf "<code>hgGcPercent -wigOut -doGaps -file=stdout -win=5 -verbose=0 test \\<br> %s | gzip -c > %s.varStep.gz</code>\n", $twoBitUrl, $accession; -} - 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 "Graph configuration help" 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> | gzip -c > $accession.gcOnFly.varStep.gz</code></b><br> +<br> + +That <b>bigWig</b> data was calculated with the <b>hgGcPercent</b> command +with the window size of <b>-win=50000</b>.<br> +<br> +To obtain the traditional 5-base window data for this track +use the following <a href='$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> $twoBitUrl \\<br> | gzip -c > ${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> | gzip -c > $accession.gc5Base.varStep.gz</code></b><br> +<br> + +Or, you can calculate that data locally at the 5-base window size +with the following <a href='$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> $twoBitUrl \\<br> | gzip -c > ${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:hiram@soe .ucsc.edu">Hiram Clawson</a>. </p> _EOF_ ;