e22f7956c30a5490adb028364bbc2c1e45b2da8b hiram Wed Nov 2 16:17:28 2022 -0700 turn off mouse strain bigMaf tracks since they do not work and now with the new style copy link to paste buffer feature for gateway description pages refs #30199 diff --git src/hg/utils/automation/asmHubGatewayPage.pl src/hg/utils/automation/asmHubGatewayPage.pl index 666dfe7..4b7454a 100755 --- src/hg/utils/automation/asmHubGatewayPage.pl +++ src/hg/utils/automation/asmHubGatewayPage.pl @@ -1,498 +1,498 @@ #!/usr/bin/env perl use strict; use warnings; use FindBin qw($Bin); use lib "$Bin"; use AsmHub; use File::Basename; ### XXX ### temporary hgdownload-test.gi ### my $sourceServer = "hgdownload-test.gi.ucsc.edu"; my $sourceServer = "hgdownload.soe.ucsc.edu"; my $genomeSize = 0; # will be set below my @months = qw( 0 Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec ); sub usage() { printf STDERR "usage: asmHubGatewayPage.pl <pathTo>/*assembly_report.txt <pathTo>/asmId.chrom.sizes <pathTo>/image.jpg <pathTo>/photoCredits.txt\n"; printf STDERR "output is to stdout, redirect to file: > description.html\n"; printf STDERR "photoCredits.txt is a two line tag<tab>string file:\n"; printf STDERR "tags: photoCreditURL and photoCreditName\n"; printf STDERR "use string 'noPhoto' for image and credits when no photo\n"; printf STDERR "stderr output is routed to a 'asmId.names.tab' file for use elsewhere\n"; exit 255; } sub chromSizes($) { my ($sizeFile) = @_; if ( -s $sizeFile ) { my $ix = 0; my $contigCount = 0; my %sizes; # key is contigName, value is size if ($sizeFile eq "stdin") { while (my $line = <>) { next if ($line =~ m/^\s*#/); ++$contigCount; chomp ($line); my ($name, $size, $rest) = split('\s+', $line, 3); my $key = sprintf("%s_X_%d", $name, $ix++); $sizes{$key} = $size; } } else { open (FH, "<$sizeFile") or die "can not read $sizeFile"; while (my $line = <FH>) { next if ($line =~ m/^\s*#/); ++$contigCount; chomp ($line); my ($name, $size, $rest) = split('\s+', $line, 3); my $key = sprintf("%s_X_%d", $name, $ix++); $sizes{$key} = $size; } close (FH); } my $totalSize = 0; foreach my $key (keys %sizes) { $totalSize += $sizes{$key} } my $n50Size = $totalSize / 2; $genomeSize = $totalSize; printf "<b>Total assembly nucleotides:</b> %s<br>\n", &AsmHub::commify($totalSize); printf "<b>Assembly contig count:</b> %s<br>\n", &AsmHub::commify($contigCount); my $prevContig = ""; my $prevSize = 0; $totalSize = 0; # work through the sizes until reaching the N50 size foreach my $key (sort { $sizes{$b} <=> $sizes{$a} } keys %sizes) { $totalSize += $sizes{$key}; if ($totalSize > $n50Size) { my $prevName = $prevContig; $prevName =~ s/_X_[0-9]+//; my $origName = $key; $origName =~ s/_X_[0-9]+//; printf "<b>N50 size:</b> %s<br>\n", &AsmHub::commify($sizes{$key}); last; } $prevContig = $key; $prevSize = $sizes{$key}; } } else { printf STDERR "# error: can not find chrom.sizes file:\n#\t'%s\'\n", $sizeFile; } } # typical reference: # ${inside}/scripts/gatewayPage.pl ${outside}/${asmReport} \ # > "${inside}/${D}/${B}.description.html" \ # 2> "${inside}/${D}/${B}.names.tab" my $argc = scalar(@ARGV); if ($argc != 4) { usage; } my ($asmReport, $chromSizes, $jpgImage, $photoCredits) = @ARGV; if ( ! -s $asmReport ) { printf STDERR "ERROR: can not find '$asmReport'\n"; usage; } if ( ! -s $chromSizes ) { printf STDERR "ERROR: can not find '$chromSizes'\n"; usage; } if ($jpgImage ne "noPhoto") { if ( ! -s $jpgImage ) { printf STDERR "ERROR: can not find '$jpgImage'\n"; usage; } if ( ! -s $photoCredits ) { printf STDERR "ERROR: can not find '$photoCredits'\n"; usage; } } my $buildDir = dirname($chromSizes); my $genesDir = "$buildDir/genes"; my $photoCreditURL = ""; my $photoCreditName = ""; my $imageSize = ""; my $imageName = ""; my $imageWidth = 0; my $imageHeight = 0; my $imageWidthBorder = 15; if ($jpgImage ne "noPhoto") { open (FH, "<$photoCredits") or die "can not read $photoCredits"; while (my $line = <FH>) { chomp $line; next if ($line =~ m/^#/); next if (length($line) < 2); my ($tag, $value) = split('\t', $line); if ($tag =~ m/photoCreditURL/) { $photoCreditURL = $value; } elsif ($tag =~ m/photoCreditName/) { $photoCreditName = $value; } } close (FH); if ( -s $jpgImage ) { $imageSize = `identify $jpgImage | awk '{print \$3}'`; chomp $imageSize; ($imageWidth, $imageHeight) = split('x', $imageSize); $imageName = basename($jpgImage); } } # transform this path name into a chrom.sizes reference my $thisDir = `pwd`; chomp $thisDir; my $ftpName = dirname($thisDir); my $asmId = basename($asmReport); $asmId =~ s/_assembly_report.txt//; my ($gcXPrefix, $accession, $rest) = split('_', $asmId, 3); my $accessionId = sprintf("%s_%s", $gcXPrefix, $accession); my $accessionDir = substr($asmId, 0 ,3); $accessionDir .= "/" . substr($asmId, 4 ,3); $accessionDir .= "/" . substr($asmId, 7 ,3); $accessionDir .= "/" . substr($asmId, 10 ,3); $accessionDir .= "/" . $accessionId; my $newStyleUrl = sprintf("%s/%s/%s/%s/%s", $gcXPrefix, substr($accession,0,3), substr($accession,3,3), substr($accession,6,3), $asmId); my $localDataUrl = sprintf("%s/%s/%s/%s/%s", $gcXPrefix, substr($accession,0,3), substr($accession,3,3), substr($accession,6,3), $accessionId); $ftpName =~ s#/hive/data/outside/ncbi/##; $ftpName =~ s#/hive/data/inside/ncbi/##; $ftpName =~ s#/hive/data/genomes/asmHubs/##; # my $urlDirectory = `basename $ftpName`; # chomp $urlDirectory; my $asmType = "genbank"; $asmType = "refseq" if ( $gcXPrefix =~ m#GCF#); my %taxIdCommonName; # key is taxId, value is common name # from NCBI taxonomy database dump open (FH, "<$ENV{'HOME'}/kent/src/hg/utils/automation/genbank/taxId.comName.tab") or die "can not read taxId.comName.tab"; while (my $line = <FH>) { chomp $line; my ($taxId, $comName) = split('\t', $line); $taxIdCommonName{$taxId} = $comName; } close (FH); my $submitter = "(n/a)"; my $asmName = "(n/a)"; my $orgName = "(n/a)"; my $taxId = "(n/a)"; my $asmDate = "(n/a)"; my $asmAccession = "(n/a)"; my $commonName = "(n/a)"; my $bioSample = "(n/a)"; my $descrAsmType = "(n/a)"; my $asmLevel = "(n/a)"; open (FH, "<$asmReport") or die "can not read $asmReport"; while (my $line = <FH>) { chomp $line; $line =~ s/ //g; if ($line =~ m/date:\s+/i) { next if ($asmDate !~ m#\(n/a#); $line =~ s/.*date:\s+//i; my ($year, $month, $day) = split('-',$line); $asmDate = sprintf("%02d %s %04d", $day, $months[$month], $year); } if ($line =~ m/biosample:\s+/i) { next if ($bioSample !~ m#\(n/a#); $line =~ s/.*biosample:\s+//i; $bioSample = $line; } if ($line =~ m/assembly\s+type:\s+/i) { next if ($descrAsmType !~ m#\(n/a#); $line =~ s/.*assembly\s+type:\s+//i; $descrAsmType = $line; } if ($line =~ m/assembly\s+level:\s+/i) { next if ($asmLevel !~ m#\(n/a#); $line =~ s/.*assembly\s+level:\s+//i; $asmLevel = $line; } if ($line =~ m/assembly\s+name:\s+/i) { next if ($asmName !~ m#\(n/a#); $line =~ s/.*assembly\s+name:\s+//i; $asmName = $line; } if ($line =~ m/organism\s+name:\s+/i) { next if ($orgName !~ m#\(n/a#); $line =~ s/.*organism\s+name:\s+//i; $line =~ s/\s+$//; $orgName = $line; } if ($line =~ m/submitter:\s+/i) { next if ($submitter !~ m#\(n/a#); $line =~ s/.*submitter:\s+//i; $submitter = $line; } if ($line =~ m/$asmType\s+assembly\s+accession:\s+/i) { next if ($asmAccession !~ m#\(n/a#); $line =~ s/.*$asmType\s+assembly\s+accession:\s+//i; $asmAccession = $line; $asmAccession =~ s/ .*//; } if ($line =~ m/taxid:\s+/i) { next if ($taxId !~ m#\(n/a#); $line =~ s/.*taxid:\s+//i; $taxId = $line; if (exists($taxIdCommonName{$taxId})) { $commonName = $taxIdCommonName{$taxId}; } } } close (FH); $commonName = $orgName if ($commonName =~ m#\(n/a#); if ($commonName =~ m/\(/) { $commonName =~ s/.*\(//; $commonName =~ s/\).*//; } if ($orgName =~ m/\(/) { $orgName =~ s/\(.*//; } $orgName =~ s/\s+$//; printf STDERR "#taxId\tcommonName\tsubmitter\tasmName\torgName\tbioSample\tasmType\tasmLevel\tasmDate\tasmAccession\n"; printf STDERR "%s\t", $taxId; printf STDERR "%s\t", $commonName; printf STDERR "%s\t", $submitter; printf STDERR "%s\t", $asmName; printf STDERR "%s\t", $orgName; printf STDERR "%s\t", $bioSample; printf STDERR "%s\t", $descrAsmType; printf STDERR "%s\t", $asmLevel; printf STDERR "%s\t", $asmDate; printf STDERR "%s\n", $asmAccession; if (length($imageName)) { printf "<!-- Display image in righthand corner --> <table align=right border=0 width=%d height=%d> <tr><td align=RIGHT><a href=\"https://www.ncbi.nlm.nih.gov/assembly/%s\" target=_blank> <img src=\"https://%s/hubs/%s/html/%s\" width=%d height=%d alt=\"%s\"></a> </td></tr> <tr><td align=right> <font size=-1> <em>%s</em><BR> </font> <font size=-2> (Photo courtesy of <a href=\"%s\" target=_blank>%s</a>) </font> </td></tr> </table> \n", $imageWidth+$imageWidthBorder, $imageHeight, $asmAccession, $sourceServer, $accessionDir, $imageName, $imageWidth, $imageHeight, $commonName, $orgName, $photoCreditURL, $photoCreditName; } my $sciNameUnderscore = $orgName; $sciNameUnderscore =~ s/ /_/g; $sciNameUnderscore = "Strigops_habroptilus" if ($orgName =~ m/Strigops habroptila/); printf "<p> -<b>Share this genome browser with the link: </b><span id='urlText'><b>https://genome.ucsc.edu/h/%s</b></span> <button class='copyLink' title='Copy URL to clipboard' id='copyIcon' data-target='urlText'><svg style='width:0.9em' xmlns='http://www.w3.org/2000/svg' viewBox='0 0 512 512'><!--! Font Awesome Pro 6.1.1 by \@fontawesome - https://fontawesome.com License - https://fontawesome.com/license (Commercial License) Copyright 2022 Fonticons, Inc. --><path d='M502.6 70.63l-61.25-61.25C435.4 3.371 427.2 0 418.7 0H255.1c-35.35 0-64 28.66-64 64l.0195 256C192 355.4 220.7 384 256 384h192c35.2 0 64-28.8 64-64V93.25C512 84.77 508.6 76.63 502.6 70.63zM464 320c0 8.836-7.164 16-16 16H255.1c-8.838 0-16-7.164-16-16L239.1 64.13c0-8.836 7.164-16 16-16h128L384 96c0 17.67 14.33 32 32 32h47.1V320zM272 448c0 8.836-7.164 16-16 16H63.1c-8.838 0-16-7.164-16-16L47.98 192.1c0-8.836 7.164-16 16-16H160V128H63.99c-35.35 0-64 28.65-64 64l.0098 256C.002 483.3 28.66 512 64 512h192c35.2 0 64-28.8 64-64v-32h-47.1L272 448z'/></svg> Copy</button><br> + <b>Share this genome browser with the link: </b><span id='urlText0'><em>https://http_host/h/%s</em></span> <span class='copyLinkSpan' data-target='urlText0'></span><br> <b>Common name:</b> %s<br> <b>Taxonomic name: %s, taxonomy ID:</b> <a href='https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=%s' target='_blank'> %s</a><br> <b>Sequencing/Assembly provider ID:</b> %s<br> <b>Assembly date:</b> %s<br> <b>Assembly type:</b> %s<br> <b>Assembly level:</b> %s<br> <b>Biosample:</b> <a href=\"https://www.ncbi.nlm.nih.gov/biosample/?term=%s\" target=\"_blank\">%s</a><br> <b>Assembly accession ID:</b> <a href=\"https://www.ncbi.nlm.nih.gov/assembly/%s\" target=\"_blank\">%s</a><br> <b>Assembly FTP location:</b> <a href='https://ftp.ncbi.nlm.nih.gov/genomes/all/%s' target='_blank'>%s</a><br> \n", $asmAccession, $commonName, $orgName, $taxId, $taxId, $submitter, $asmDate, $descrAsmType, $asmLevel, $bioSample, $bioSample, $asmAccession, $asmAccession, $newStyleUrl, $newStyleUrl; chromSizes($chromSizes); printf "</p>\n<hr> <h4>Data file downloads</h4> <p> <ul> <li><a href='https://$sourceServer/hubs/$localDataUrl/$asmAccession.fa.gz' target=_blank>$asmAccession.fa.gz</a> fasta sequence with NCBI GenBank sequence names</li> <li><a href='https://$sourceServer/hubs/$localDataUrl/$asmAccession.2bit' target=_blank>$asmAccession.2bit</a> UCSC 2bit sequence file with NCBI GenBank sequence names</li> <li><a href='https://$sourceServer/hubs/$localDataUrl/$asmAccession.chromAlias.txt' target=_blank>$asmAccession.chromAlias.txt</a> chromAlias file to relate chromosome names</li> "; if ( -s "$buildDir/$asmId.chrNames.fa.gz") { printf "<li><a href='https://$sourceServer/hubs/$localDataUrl/$asmAccession.chrNames.fa.gz' target=_blank>$asmAccession.chrNames.fa.gz</a> fasta sequence with <b>chrN</b> sequence names</li>\n"; } if ( -s "$buildDir/$asmId.chrNames.2bit") { printf "<li><a href='https://$sourceServer/hubs/$localDataUrl/$asmAccession.chrNames.2bit' target=_blank>$asmAccession.chrNames.2bit</a> UCSC 2bit sequence file with <b>chrN</b> sequence names</li>\n"; } if ( -d "$genesDir" ) { open (GD, "ls $genesDir/*.gtf.gz $genesDir/*.gff3.gz 2> /dev/null|") or die "can not ls $genesDir/*.gtf.gz"; while (my $gtfFile = <GD>) { chomp $gtfFile; my $gtf = basename($gtfFile); if ($gtf =~ m/gff3.gz/) { printf "<li><a href='https://$sourceServer/hubs/$localDataUrl/genes/$gtf' target=_blank>$gtf</a> gene GFF3 file</li>\n"; } else { printf "<li><a href='https://$sourceServer/hubs/$localDataUrl/genes/$gtf' target=_blank>$gtf</a> gene GTF file</li>\n"; } } close (GD); } if ( -d "${buildDir}/otherAligners" ) { printf "<li><a href='https://$sourceServer/hubs/$localDataUrl/otherAligners/' target=_blank>pre-computed indices</a> for alignment programs: bowtie2, bwa-mem2, hisat2, minimap2</li>\n"; } printf "<li>explore the hub directory at: <a href='https://$sourceServer/hubs/$localDataUrl/' target=_blank>$sourceServer/hubs/$localDataUrl/</a></li> </ul> "; printf "</p>\n<hr> <h4>Copy this entire assembly hub for local use</h4> <p> This download is only for the purpose of using this assembly hub in your institution which may have firewall access restrictions to this data.<br> To download this assembly data, use this <b>rsync</b> command: <pre> rsync -a -P \\ rsync://$sourceServer/hubs/$localDataUrl/ \\ ./$accessionId/ </pre> which creates the local directory: <b>./$accessionId/</b><br> or this <b>wget</b> command: <pre> wget --timestamping -m -nH -x --cut-dirs=6 -e robots=off -np -k \\ --reject \"index.html*\" -P \"$accessionId\" \\ https://$sourceServer/hubs/$localDataUrl/ </pre> which creates a local directory: <b>./$accessionId/</b> <p> There is an included <b>hub.txt</b> file in that download data directory to use for your local track hub instance.<br> Using the genome browser menus: <em><strong>My Data</strong> -> <strong>Track Hubs</strong></em><br> select the <em><strong>My Hubs</strong></em> tab to enter a URL to this <b>hub.txt</b> file to attach this assembly hub to a genome browser. </p> <p> The <b>html/$asmId.description.html</b> page is information for your users to describe this assembly.<br>This web page with these instructions is an instance of the <b>html/$asmId.description.html</b> file. </p> <p> See also: <a href='/goldenPath/help/hgTrackHubHelp.html' target=_blank>track hub help</a> documentation.<br> </p>\n"; if ($genomeSize < 4294967297) { printf "<hr> <h4>blat service</h4> <p> There is blat service available for this genome assembly. When viewing this assembly in the genome browser, access the blat service via the <em><b>Tools -> Blat</b></em> blue navigation bar menu item. </p> <p> For local command line blat service, access the blat service via the <b>gfClient</b> command line operation.<br> See also: <a href='http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/' target=_blank> hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/</a> to download command line binaries.<br> <br> To operate this locally, you will need the <b>$accessionId.2bit</b> file from: <pre> https://$sourceServer/hubs/$localDataUrl/ </pre> Which can be obtained with rsync via: <pre> rsync -a -P \ rsync://hgdownload.soe.ucsc.edu/hubs/$accessionDir/$accessionId.2bit ./ </pre> With that <b>$accessionId.2bit</b> file in your working directory where you run this command, for example, a DNA query with your DNA sequence in the file: <b>someDna.fa</b> with result in the file: <b>$accessionId.someDna.psl</b> <pre> gfClient -t=dna -q=dna -genome=$accessionId -genomeDataDir=$accessionDir \ dynablat-01.soe.ucsc.edu 4040 ./ someDna.fa $accessionId.someDna.psl </pre> For a protein fasta query with your protein sequence in the file: <b>someProtein.faa</b> with result in the file: <b>$accessionId.someProtein.psl</b> <pre> gfClient -t=dnax -q=prot -genome=$accessionId -genomeDataDir=$accessionDir \ dynablat-01.soe.ucsc.edu 4040 ./ someProtein.faa $accessionId.someProtein.psl </pre> </p>\n"; } else { printf "<hr> <p> At this time, this genome size: %s, is too large (greater than 4294967296), to function with the UCSC blat system. We hope to have improvements to that system in the future to allow blat service for the larger genome sizes. </p>\n", &AsmHub::commify($genomeSize); } printf "<hr> <p> <b>Search the assembly:</b> <ul> <li> <b>By position or search term: </b> Use the "position or search term" box to find areas of the genome associated with many different attributes, such as a specific chromosomal coordinate range; mRNA, EST, or STS marker names; or keywords from the GenBank description of an mRNA. <a href=\"http://genome.ucsc.edu/goldenPath/help/query.html\">More information</a>, including sample queries.</li> <li> <b>By gene name: </b> Type a gene name into the "search term" box, choose your gene from the drop-down list, then press "submit" to go directly to the assembly location associated with that gene. <a href=\"http://genome.ucsc.edu/goldenPath/help/geneSearchBox.html\">More information</a>. To avoid case sensitivity issues, always use fully lower case gene names.</li> <li> <b>By track type: </b> Click the "track search" button to find Genome Browser tracks that match specific selection criteria. <a href=\"http://genome.ucsc.edu/goldenPath/help/trackSearch.html\">More information</a>.</li> </ul> </p> <hr>\n"; __END__ /hive/data/outside/ncbi/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.30_GRCh38.p4/GCF_000001405.30_GRCh38.p4_assembly_report.txt # Assembly Name: GRCh38.p4 # Description: Genome Reference Consortium Human Build 38 patch release 4 (GRCh38.p4) # Organism name: Homo sapiens (human) # Taxid: 9606 # Submitter: Genome Reference Consortium # Date: 2015-6-25 # Assembly type: haploid-with-alt-loci # Release type: patch # Assembly level: Chromosome # Genome representation: full # GenBank Assembly Accession: GCA_000001405.19 (latest) # RefSeq Assembly Accession: GCF_000001405.30 (latest) # RefSeq Assembly and GenBank Assemblies Identical: yes # ## Assembly-Units: ## GenBank Unit Accession RefSeq Unit Accession Assembly-Unit name ## GCA_000001305.2 GCF_000001305.14 Primary Assembly ## GCA_000005045.17 GCF_000005045.16 PATCHES ## GCA_000001315.2 GCF_000001315.2 ALT_REF_LOCI_1