790b166f17ba0ef2f8cfe220dbc6c2a67035ede9 hiram Wed Mar 15 21:16:40 2023 -0700 adding HPRC links to the index pages refs #30508 diff --git src/hg/makeDb/doc/asmHubs/trackData.pl src/hg/makeDb/doc/asmHubs/trackData.pl index 2b0a2f6..8b8b7b9 100755 --- src/hg/makeDb/doc/asmHubs/trackData.pl +++ src/hg/makeDb/doc/asmHubs/trackData.pl @@ -37,30 +37,32 @@ } my $Name = shift; my $asmHubName = shift; my $inputList = shift; my $orderList = $inputList; if ( ! -s "$orderList" ) { $orderList = $toolsDir/$inputList; } my @orderList; # asmId of the assemblies in order from the orderList file my %commonName; # key is asmId, value is a common name, perhaps more appropriate # than found in assembly_report file # assembly_report my $vgpIndex = 0; $vgpIndex = 1 if ($Name =~ m/vgp/i); +my $hprcIndex = 0; +$hprcIndex = 1 if ($Name =~ m/hprc/i); my $assemblyTotal = 0; # complete list of assemblies in this group my $asmCount = 0; # count of assemblies completed and in the table my $overallNucleotides = 0; my $overallSeqCount = 0; my $overallGapSize = 0; my $overallGapCount = 0; ############################################################################## # from Perl Cookbook Recipe 2.17, print out large numbers with comma delimiters: ############################################################################## sub commify($) { my $text = reverse $_[0]; $text =~ s/(\d\d\d)(?=\d)(?!\d*\.)/$1,/g; return scalar reverse $text @@ -155,44 +157,65 @@ <!--#include virtual="\$ROOT/inc/gbPageStartHardcoded.html" --> <h1>VGP - Vertebrate Genomes Project assembly hubs, track statistics</h1> <p> <a href='https://vertebrategenomesproject.org/' target=_blank> <img src='VGPlogo.png' width=280 alt='VGP logo'></a></p> <p> This assembly hub contains assemblies released by the <a href='https://vertebrategenomesproject.org/' target=_blank> Vertebrate Genomes Project.</a> $vgpSubset </p> END } else { + if ($hprcIndex) { + print <<"END" +<!DOCTYPE HTML 4.01 Transitional> +<!--#set var="TITLE" value="HPRC - Human Pangenome Reference Consortium assembly hubs, track statistics" --> +<!--#set var="ROOT" value="../.." --> + +<!--#include virtual="\$ROOT/inc/gbPageStartHardcoded.html" --> + +<h1>HPRC - Human Pangenome Reference Consortium assembly hubs, track statistics</h1> +<p> +<a href='https://humanpangenome.org/' target=_blank> +<img src='HPRC_logo.png' width=280 alt='HPRC logo'></a></p> +<p> +This assembly hub contains assemblies released +by the <a href='https://humanpangenome.org/' target=_blank> +Human Pangenome Reference Consortium.</a> +</p> + +END + } else { print <<"END" <!DOCTYPE HTML 4.01 Transitional> <!--#set var="TITLE" value="$Name genomes assembly hubs, track statistics" --> <!--#set var="ROOT" value="../.." --> <!--#include virtual="\$ROOT/inc/gbPageStartHardcoded.html" --> <h1>$Name Genomes assembly hubs, track statistics</h1> <p> Assemblies from NCBI/Genbank/Refseq sources, $subSetMessage. </p> END } +} my $indexUrl = "index"; my $asmStats = "asmStats"; print <<"END" <h3>See also: <a href='$indexUrl.html'>hub access</a>, <a href='$asmStats.html'>assembly statistics</a></h3><br> <h3>Data resource links</h3> NOTE: <em>Click on the column headers to sort the table by that column</em><br> The <em>link to genome browser</em> will attach only that single assembly to the genome browser.<br> The numbers are: item count (percent coverage)<br> Except for the gc5Base column which is: overall GC % average (percent coverage) END } # sub startHtml() # order of columns in the table