8ccd7b6237d9d6d6113a0c97087471874ccb0d8f hiram Fri Apr 28 15:08:23 2023 -0700 add the CCGP to the index listing table refs #30508 diff --git src/hg/makeDb/doc/asmHubs/commonHtml.pm src/hg/makeDb/doc/asmHubs/commonHtml.pm index 2f3e2fe..c3be265 100644 --- src/hg/makeDb/doc/asmHubs/commonHtml.pm +++ src/hg/makeDb/doc/asmHubs/commonHtml.pm @@ -1,132 +1,140 @@ package commonHtml; # helper functions for common HTML output features use warnings; use strict; use Carp; use vars qw(@ISA @EXPORT_OK); use Exporter; @ISA = qw(Exporter); # This is a listing of the public methods and variables (which should be # treated as constants) exported by this module: @EXPORT_OK = ( qw( otherHubLinks htmlFooter ) ); # otherHubLinks: arg one: vgpIndex, arg two: asmHubName, arg three: orderList # arguments allow decision on customization of the table for different # types of assembly hubs sub otherHubLinks($$) { my ($vgpIndex, $asmHubName) = @_; my %asmCounts; # key is hubName, value is number of assemblies my @hubList = qw(primates mammals birds fish vertebrate invertebrate plants fungi viral bacteria); foreach my $hubName (@hubList) { my $asmCount = `grep -v "^#" ../${hubName}AsmHub/${hubName}.orderList.tsv | wc -l`; chomp $asmCount; $asmCounts{$hubName} = $asmCount; } my $vgpCount = `grep -h -v "^#" ../vgpAsmHub/vgp.*.orderList.tsv | wc -l`; chomp $vgpCount; $asmCounts{'vgp'} = $vgpCount; my $hprcCount = `grep -c -h -v "^#" ../hprcAsmHub/hprc.orderList.tsv`; chomp $hprcCount; $asmCounts{'hprc'} = $hprcCount; +my $ccgpCount = `grep -c -h -v "^#" ../ccgpAsmHub/ccgp.orderList.tsv`; +chomp $ccgpCount; +$asmCounts{'ccgp'} = $ccgpCount; my $legacyCount = `grep -c -h -v "^#" ../legacyAsmHub/legacy.orderList.tsv`; chomp $legacyCount; $asmCounts{'legacy'} = $legacyCount; # different table output for VGP index if ((0 == $vgpIndex)) { printf "<p>\n<table border='1' style='margin-left:auto; margin-right:auto;'><thead>\n"; printf "<tr><th colspan=4 style='text-align:center;'>Additional hubs with collections of assemblies</th></tr>\n"; printf "<tr><th>Collection</th>\n"; printf " <th>Hub index pages:</th>\n"; printf " <th>Assembly statistics:</th>\n"; printf " <th>Track statistics:</th>\n"; printf "</tr>\n"; foreach my $hubName (@hubList) { if ($hubName =~ m/^vertebrate/) { printf "<tr><th>other vertebrates</th>\n"; } elsif ($hubName =~ m/fish/) { printf "<tr><th>Fishes</th>\n"; } elsif ($hubName =~ m/invertebrate/) { printf "<tr><th>Invertebrates</th>\n"; } elsif ($hubName =~ m/viral/) { printf "<tr><th>Viruses</th>\n"; } elsif ($hubName =~ m/bacteria/) { printf "<tr><th>Bacteria</th>\n"; } else { printf "<tr><th>%s</th>\n", ucfirst($hubName); } printf " <th style='text-align:right'><a href='../%s/index.html'>%d assemblies</a></th>\n", $hubName, $asmCounts{$hubName}; printf " <th><a href='../%s/asmStats.html'>assembly stats</a></th>\n", $hubName; printf " <th><a href='../%s/trackData.html'>track stats</a></th>\n", $hubName; printf "</tr>\n"; } printf "<tr><th>VGP - Vertebrate Genome Project</th>\n"; printf " <th style='text-align:right'><a href='../%s/index.html'>%d assemblies</a></th>\n", "VGP", $asmCounts{'vgp'}; printf " <th><a href='../VGP/asmStats.html'>assembly stats</a></th>\n"; printf " <th><a href='../VGP/trackData.html'>track stats</a></th>\n"; printf "</tr>\n"; + printf "<tr><th>CCGP - The California Conservation Genomics Project</th>\n"; + printf " <th style='text-align:right'><a href='../%s/index.html'>%d assemblies</a></th>\n", "CCGP", $asmCounts{'ccgp'}; + printf " <th><a href='../CCGP/asmStats.html'>assembly stats</a></th>\n"; + printf " <th><a href='../CCGP/trackData.html'>track stats</a></th>\n"; + printf "</tr>\n"; printf "<tr><th>HPRC - Human Pangenome Reference Consortium</th>\n"; printf " <th style='text-align:right'><a href='../%s/index.html'>%d assemblies</a></th>\n", "HPRC", $asmCounts{'hprc'}; printf " <th><a href='../HPRC/asmStats.html'>assembly stats</a></th>\n"; printf " <th><a href='../HPRC/trackData.html'>track stats</a></th>\n"; printf "</tr>\n"; printf "<tr><th>legacy/superseded</th>\n"; printf " <th style='text-align:right'><a href='../%s/index.html'>%d assemblies</a></th>\n", "legacy", $asmCounts{'legacy'}; printf " <th><a href='../legacy/asmStats.html'>assembly stats</a></th>\n"; printf " <th><a href='../legacy/trackData.html'>track stats</a></th>\n"; printf "</tr></thead>\n</table>\n</p>\n"; } elsif (1 == $vgpIndex) { printf "<p>\n<table border='1'><thead>\n"; printf "<tr><th colspan=5 style='text-align:center;'>Alternate sets of VGP assemblies</th><th style='text-align:center;'>NCBI Refseq</th></tr>\n"; printf "<tr><th>Index pages: </th>\n"; printf "<th><a href='index.html'>primary assembly</a></th>\n"; printf "<th><a href='vgpAlt.html'>alternate/haplotype</a></th>\n"; printf "<th><a href='vgpTrio.html'>trio mat/pat</a></th>\n"; printf "<th><a href='vgpLegacy.html'>legacy/superseded</a></th>\n"; printf "<th><a href='../primates/index.html'>other NCBI Refseq assemblies</a></th>\n"; printf "</tr><tr>\n"; printf "<th>Assembly statistics: </th>\n"; printf "<th><a href='asmStats.html'>primary assembly</a></th>\n"; printf "<th><a href='vgpAltStats.html'>alternate/haplotype</a></th>\n"; printf "<th><a href='vgpTrioStats.html'>trio mat/pat</a></th>\n"; printf "<th><a href='vgpLegacyStats.html'>legacy/superseded</a></th>\n"; printf "<th><a href='../primates/asmStats.html'>other NCBI Refseq assemblies</a></th>\n"; printf "</tr><tr>\n"; printf "<th>Track statistics: </th>\n"; printf "<th><a href='trackData.html'>primary assembly</a></th>\n"; printf "<th><a href='vgpAltData.html'>alternate/haplotype</a></th>\n"; printf "<th><a href='vgpTrioData.html'>trio mat/pat</a></th>\n"; printf "<th><a href='vgpLegacyData.html'>legacy/superseded</a></th>\n"; printf "<th><a href='../primates/trackData.html'>other NCBI Refseq assemblies</a></th>\n"; printf "</tr><tr>\n"; printf "</tr></thead>\n</table>\n</p>\n"; } } # sub otherHubLinks($$) ############################################################################ # common output at the bottom of an html index page sub htmlFooter() { print <<"END" </div><!-- closing gbsPage from gbPageStartHardcoded.html --> </div><!-- closing container-fluid from gbPageStartHardcoded.html --> <!--#include virtual="\$ROOT/inc/gbFooterHardcoded.html"--> <script type="text/javascript" src="<!--#echo var="ROOT" -->/js/sorttable.js"></script> </body></html> END } ############################################################################