c316bef9ca9fbaac700de97a076a46297102166f hiram Thu Apr 15 13:55:04 2021 -0700 now with title GenArk: UCSC Genome Archive and counting taxIds before and after update refs #23891 diff --git src/hg/makeDb/doc/asmHubs/hubIndex.pl src/hg/makeDb/doc/asmHubs/hubIndex.pl index d360318..a63fc75 100755 --- src/hg/makeDb/doc/asmHubs/hubIndex.pl +++ src/hg/makeDb/doc/asmHubs/hubIndex.pl @@ -1,184 +1,184 @@ #!/usr/bin/env perl use strict; use warnings; use File::Basename; my $thisMachine = `uname -n`; chomp $thisMachine; if ($thisMachine ne "hgdownload") { printf STDERR "# NOTE: This script is only used on hgdownload\n"; exit 255; } ############################################################################# sub startHtml() { printf ' - + -

UCSC Genome Browser Assembly hubs

+

GenArk: UCSC Genome Archive

' } ############################################################################# sub endHtml() { printf ' ' } ############################################################################# startHtml; my %expectedList = ( "VGP" => 1, "birds" => 1, "fish" => 1, "globalReference" => 1, "mammals" => 1, "primates" => 1, "vertebrate" => 1, "invertebrate" => 1, "fungi" => 1, "legacy" => 1, "plants" => 1, ); my %titles = ( "VGP" => "Vertebrate Genomes Project collection", "birds" => "NCBI bird genomes", "fish" => "NCBI fish genomes", "globalReference" => "Global Human Reference genomes, January 2020", "mammals" => "NCBI mammal genomes", "primates" => "NCBI primate genomes", "vertebrate" => "NCBI other vertebrate genomes", "invertebrate" => "NCBI invertebrate genomes", "fungi" => "NCBI fungi genomes", "legacy" => "NCBI genomes legacy/superseded by newer versions", "plants" => "NCBI plant genomes", "gtexAnalysis" => "Genotype-Tissue Expression (GTEx) Project analysis results track hub, V6 October 2015", "gtex" => "Genotype-Tissue Expression (GTEx) RNA-seq signal track hub, V6 October 2015", "mouseStrains" => "16 mouse strain assembly and track hub, May 2017", "neuroDiffCrispr" => "Structurally conserved primate cerebral cortex lincRNAs track hub, December 2018", ); my %otherTopLevels = ( "GCA" => 1, "GCF" => 1, "gtex" => 1, "gtexAnalysis" => 1, "mouseStrains" => 1, "neuroDiffCrispr" => 1, "UCSC_GI.assemblyHubList.txt" => 1, "index.html" => 1, ); my @orderOutHubs = ( "primates", "mammals", "birds", "fish", "vertebrate", "invertebrate", "fungi", "plants", "VGP", "globalReference", "mouseStrains", "legacy", ); my @orderOutTracks = ( "gtexAnalysis", "gtex", "neuroDiffCrispr", ); my %indexPage = ( "primates" => "index.html", "mammals" => "index.html", "birds" => "index.html", "fish" => "index.html", "vertebrate" => "index.html", "invertebrate" => "index.html", "fungi" => "index.html", "legacy" => "index.html", "plants" => "index.html", "VGP" => "index.html", "mouseStrains" => "hubIndex.html", "globalReference" => "index.html", "gtexAnalysis" => "index.html", "gtex" => "index.html", "neuroDiffCrispr" => "index.html", ); # verify all known directories and files, alert for any new ones open (FH, "ls -d /mirrordata/hubs/*|") or die "can not ls -d /mirrordata/hubs/*"; while (my $dirPath = ) { chomp $dirPath; my $fileDirName = basename($dirPath); if (! (defined($expectedList{$fileDirName}) || defined($otherTopLevels{$fileDirName})) ) { printf STDERR "# something new: %s\n", $fileDirName; } } close (FH); ### Determine genome counts: my %genomeCounts; my $genomeCount = `grep -h ^genome /mirrordata/hubs/VGP/*enomes.txt | wc -l`; chomp $genomeCount; $genomeCounts{"VGP"} = $genomeCount; my @checkList = ('primates', 'mammals', 'birds', 'fish', 'vertebrate', 'legacy', 'plants', "invertebrate", "fungi", 'globalReference'); foreach my $hubSet (@checkList) { $genomeCount = `grep -h ^genome /mirrordata/hubs/$hubSet/genomes.txt | wc -l`; chomp $genomeCount; $genomeCounts{$hubSet} = $genomeCount; } my $hubCount = 0; printf "\n"; printf "\n"; printf " \n"; printf " \n"; printf "\n"; # construct table foreach my $orderUp (@orderOutHubs) { printf "\n"; ++$hubCount; if ($orderUp eq "fish") { printf " \n", $orderUp, $indexPage{$orderUp}; } else { printf " \n", $orderUp, $indexPage{$orderUp}, $orderUp; } if (defined($genomeCounts{$orderUp})) { printf " \n", $titles{$orderUp}, $genomeCounts{$orderUp}; } else { printf " \n", $titles{$orderUp}; } printf "\n"; } printf "
hub gatewaydescription
fishes%s%s (%d assemblies)%s
\n"; my $totalAsmHubs = `grep -v "^#" /mirrordata/hubs/UCSC_GI.assemblyHubList.txt | wc -l`; chomp $totalAsmHubs; printf "

\n"; printf "Please note: text file listing of %d NCBI/VGP genome assembly hubs\n", $totalAsmHubs; printf "

\n"; endHtml;