636dc23e0f0b10bb1f1be27b7936ec15b9be2f49 hiram Wed Jul 29 21:53:06 2026 -0700 hub link to the archive without duplicating the tracks refs #37958 diff --git src/hg/utils/automation/AsmHub.pm src/hg/utils/automation/AsmHub.pm index 035f949ab61..9cab4a83f87 100755 --- src/hg/utils/automation/AsmHub.pm +++ src/hg/utils/automation/AsmHub.pm @@ -1,169 +1,169 @@ # AsmHub: common routines for building assembly hubs # # DO NOT EDIT the /cluster/bin/scripts copy of this file -- # edit ~/kent/src/hg/utils/automation/AsmHub.pm instead. package AsmHub; use warnings; use strict; use Carp; use File::Basename; 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 = ( # Support for common command line options: qw( commify asmSize ncbiGeneDescription ), ); # from Perl Cookbook Recipe 2.17, print out large numbers with comma # delimiters, input is a large number with no commas: sub commify($) { my $text = reverse $_[0]; $text =~ s/(\d\d\d)(?=\d)(?!\d*\.)/$1,/g; return scalar reverse $text } # given an asmId.chrom.sizes, return the assembly size from the # sum of column 2: sub asmSize($) { my ($chromSizes) = @_; my $asmSize=`/cluster/bin/x86_64/ave -col=2 $chromSizes | grep "total" | sed -e 's/total //; s/.000000//;'`; chomp $asmSize; return $asmSize; } # given a fully qualified asmId, e.g.: GCA_018504075.1_HG02723.alt.pat.f1_v2 # return the string representating the path: GCA/018/504/075 sub asmIdToPath($) { my ($asmId) = @_; my $gcX = substr($asmId, 0, 3); my $d0 = substr($asmId, 4, 3); my $d1 = substr($asmId, 7, 3); my $d2 = substr($asmId, 10, 3); my $ret = sprintf("%s/%s/%s/%s", $gcX, $d0, $d1, $d2); return $ret; } # Build the 'ncbiGene' track description HTML body. Used both by # asmHubNcbiGene.pl for the live track, and by doNcbiGene.pl for the # one-track archive hubs it writes under trackData/ncbiGene/archive/ -- # which is why every path is taken explicitly rather than assumed from # the usual trackData/ layout. $archiveNote, if given, is printed as a # lead-in banner ahead of the normal description (used for the archived # copies; the live page passes it undef). sub ncbiGeneDescription($$$$$;$) { my ($bbPath, $statsPath, $chromSizes, $namesFile, $ncbiAsmId, $archiveNote) = @_; if ( ! -s $bbPath ) { printf STDERR "ERROR: can not find %s file\n", $bbPath; exit 255; } my @partNames = split('_', $ncbiAsmId); my $ftpDirPath = sprintf("%s/%s/%s/%s/%s", $partNames[0], substr($partNames[1],0,3), substr($partNames[1],3,3), substr($partNames[1],6,3), $ncbiAsmId); my $asmType = ($partNames[0] =~ m/GCA/) ? "genbank" : "refseq"; my $totalBases = asmSize($chromSizes); my $geneStats = `cat $statsPath | awk '{printf "%d\\n", \$2}' | xargs echo`; chomp $geneStats; my ($itemCount, $basesCovered) = split('\s+', $geneStats); my $percentCoverage = sprintf("%.3f", 100.0 * $basesCovered / $totalBases); $itemCount = commify($itemCount); $basesCovered = commify($basesCovered); my $totalBasesText = commify($totalBases); my $em = "<em>"; my $noEm = "</em>"; my $assemblyDate = `grep -v "^#" $namesFile | cut -f9`; chomp $assemblyDate; my $organism = `grep -v "^#" $namesFile | cut -f5`; chomp $organism; my $html = ""; $html .= "<p><b>$archiveNote</b></p>\n\n" if ($archiveNote); if ( "${asmType}" eq "refseq" ) { $html .= <<_EOF_; <h2>Description</h2> <p> The NCBI Gene track for the $assemblyDate $em${organism}$noEm/$ncbiAsmId genome assembly is constructed from the gff file <b>${ncbiAsmId}_genomic.gff.gz</b> supplied with the genome assembly at the FTP location:<br> <a href='https://ftp.ncbi.nlm.nih.gov/genomes/all/$ftpDirPath/' target='_blank'>https://ftp.ncbi.nlm.nih.gov/genomes/all/$ftpDirPath/</a> </p> _EOF_ } else { $html .= <<_EOF_; <h2>Description</h2> <p> The Gene model track for the $assemblyDate $em${organism}$noEm/$ncbiAsmId genome assembly is constructed from the gff file <b>${ncbiAsmId}_genomic.gff.gz</b> supplied with the genome assembly at the FTP location:<br> <a href='https://ftp.ncbi.nlm.nih.gov/genomes/all/$ftpDirPath/' target='_blank'>https://ftp.ncbi.nlm.nih.gov/genomes/all/$ftpDirPath/</a> </p> <p> The gene models were constructed by the submitter of the assembly to the NCBI assembly release system. </p> _EOF_ } $html .= <<_EOF_; <h2>Track statistics summary</h2> <p> <b>Total genome size: </b>$totalBasesText<br> <b>Gene count: </b>$itemCount<br> <b>Bases in genes: </b>$basesCovered<br> <b>Percent genome coverage: </b>% $percentCoverage<br> </p> _EOF_ # Only the live page advertises archives (an archived page's own # description already carries $archiveNote and has nothing further # under it to list). Archived copies are published to hgdownload at # https://hgdownload.soe.ucsc.edu/hubs/<hashedPath>/<accession>/archive/ncbiGene/<version>/hub.txt # -- one self-contained hub.txt per version -- regardless of where they # sit in the local build tree, so we just need the version list. if ( ! $archiveNote ) { my $archiveBase = dirname($bbPath) . "/archive"; my @versions = (); if ( -d $archiveBase ) { opendir(my $dh, $archiveBase); if ($dh) { @versions = sort { $b cmp $a } grep { -d "$archiveBase/$_" && $_ !~ m/^\./ } readdir($dh); closedir($dh); } } if (@versions) { my @parts = split('_', $ncbiAsmId); my $accession = "$parts[0]_$parts[1]"; my $hashedPath = asmIdToPath($ncbiAsmId); $html .= "<h2>Archived versions</h2>\n<p>\n"; $html .= "Earlier versions of this track, from before NCBI updated the source annotation, remain available as standalone track hubs:\n"; $html .= "</p>\n<ul>\n"; foreach my $version (@versions) { my $hubUrl = "https://hgdownload.soe.ucsc.edu/hubs/$hashedPath/$accession/archive/ncbiGene/$version/hub.txt"; - my $url = "/h/$accession?hubUrl=$hubUrl"; + my $url = "/cgi-bin/hgTracks?genome=$accession&hubUrl=$hubUrl"; $html .= "<li><a href='$url' target='_blank'>$version</a></li>\n"; } $html .= "</ul>\n\n"; } } return $html; } # ncbiGeneDescription 1;