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/commonHtml.pm src/hg/makeDb/doc/asmHubs/commonHtml.pm index 6be84f6..2f3e2fe 100644 --- src/hg/makeDb/doc/asmHubs/commonHtml.pm +++ src/hg/makeDb/doc/asmHubs/commonHtml.pm @@ -13,75 +13,85 @@ # 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); +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 $legacyCount = `grep -h -v "^#" ../legacyAsmHub/legacy.orderList.tsv | wc -l`; +my $hprcCount = `grep -c -h -v "^#" ../hprcAsmHub/hprc.orderList.tsv`; +chomp $hprcCount; +$asmCounts{'hprc'} = $hprcCount; +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>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";