6964f094f71a69fa083dbe3a6d88dc84f60b0855 hiram Thu Feb 25 11:44:28 2021 -0800 expanded link to other hubs table refs #23891 diff --git src/hg/makeDb/doc/asmHubs/commonHtml.pm src/hg/makeDb/doc/asmHubs/commonHtml.pm index 0697f76..9ff8c94 100644 --- src/hg/makeDb/doc/asmHubs/commonHtml.pm +++ src/hg/makeDb/doc/asmHubs/commonHtml.pm @@ -12,84 +12,104 @@ # 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); +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`; +chomp $legacyCount; +$asmCounts{'legacy'} = $legacyCount; + # different table output for VGP index if ((0 == $vgpIndex) && ($asmHubName ne "viral")) { - printf "<p>\n<table border='1'><thead>\n"; - printf "<tr><th colspan=7 style='text-align:center;'>Additional hubs with collections of assemblies</th></tr>\n"; - printf "<tr><th>Assembly hubs index pages: </th>\n"; - printf "<th><a href='../primates/index.html'>Primates</a></th>\n"; - printf "<th><a href='../mammals/index.html'>Mammals</a></th>\n"; - printf "<th><a href='../birds/index.html'>Birds</a></th>\n"; - printf "<th><a href='../fish/index.html'>Fish</a></th>\n"; - printf "<th><a href='../vertebrate/index.html'>other vertebrates</a></th>\n"; - printf "<th><a href='../legacy/index.html'>legacy/superseded</a></th>\n"; - - printf "</tr><tr>\n"; - printf "<th>Hubs assembly statistics: </th>\n"; - printf "<th><a href='../primates/asmStats.html'>Primates</a></th>\n"; - printf "<th><a href='../mammals/asmStats.html'>Mammals</a></th>\n"; - printf "<th><a href='../birds/asmStats.html'>Birds</a></th>\n"; - printf "<th><a href='../fish/asmStats.html'>Fish</a></th>\n"; - printf "<th><a href='../vertebrate/asmStats.html'>other vertebrates</a></th>\n"; - printf "<th><a href='../legacy/asmStats.html'>legacy/superseded</a></th>\n"; - - printf "</tr><tr>\n"; - printf "<th>Hubs track statistics: </th>\n"; - printf "<th><a href='../primates/trackData.html'>Primates</a></th>\n"; - printf "<th><a href='../mammals/trackData.html'>Mammals</a></th>\n"; - printf "<th><a href='../birds/trackData.html'>Birds</a></th>\n"; - printf "<th><a href='../fish/trackData.html'>Fish</a></th>\n"; - printf "<th><a href='../vertebrate/trackData.html'>other vertebrates</a></th>\n"; - printf "<th><a href='../legacy/trackData.html'>legacy/superseded</a></th>\n"; - + 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"; + } 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>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></tr>\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"-->