19d33fe8c7b5b90b7faa514185c79eb6af0d8d8b hiram Tue Jan 21 13:22:47 2020 -0800 now using new style GCF path names and separate hubs for each assembly refs #24748 diff --git src/hg/makeDb/doc/primateAsmHub/mkGenomes.pl src/hg/makeDb/doc/primateAsmHub/mkGenomes.pl index 41302c3..0736e31 100755 --- src/hg/makeDb/doc/primateAsmHub/mkGenomes.pl +++ src/hg/makeDb/doc/primateAsmHub/mkGenomes.pl @@ -1,127 +1,182 @@ #!/usr/bin/env perl use strict; use warnings; use File::Basename; my %betterName; # key is asmId, value is common name my $hubName = "primates"; my $srcDocDir = "primateAsmHub"; my $buildDir = "/hive/data/genomes/asmHubs/refseqBuild"; my $destDir = "/hive/data/genomes/asmHubs/$hubName"; my $home = $ENV{'HOME'}; my $srcDir = "$home/kent/src/hg/makeDb/doc/$srcDocDir"; my $commonNameList = "primates.asmId.commonName.tsv"; my $commonNameOrder = "primates.commonName.asmId.orderList.tsv"; open (FH, "<$srcDir/${commonNameList}") or die "can not read $srcDir/${commonNameList}"; while (my $line = <FH>) { chomp $line; my ($asmId, $name) = split('\t', $line); $betterName{$asmId} = $name; } close (FH); my @orderList; # asmId of the assemblies in order from the *.list files # the order to read the different .list files: my $assemblyCount = 0; open (FH, "<$srcDir/${commonNameOrder}") or die "can not read ${commonNameOrder}"; while (my $line = <FH>) { chomp $line; my ($commonName, $asmId) = split('\t', $line); push @orderList, $asmId; ++$assemblyCount; } close (FH); my $orderKey = 1; foreach my $asmId (reverse(@orderList)) { my $buildDir = "/hive/data/genomes/asmHubs/refseqBuild/" . substr($asmId, 0 ,3); $buildDir .= "/" . substr($asmId, 4 ,3); $buildDir .= "/" . substr($asmId, 7 ,3); $buildDir .= "/" . substr($asmId, 10 ,3); $buildDir .= "/" . $asmId; my $asmReport="$buildDir/download/${asmId}_assembly_report.txt"; my $descr=`grep -i "organism name:" $asmReport | head -1 | sed -e 's#.*organism name: *##i; s# (.*\$##;'`; chomp $descr; my $orgName=`grep -i "organism name:" $asmReport | head -1 | sed -e 's#.* name: .* (##; s#).*##;'`; chomp $orgName; $orgName = $betterName{$asmId} if (exists($betterName{$asmId})); printf "genome %s\n", $asmId; printf "trackDb genomes/%s/%s.trackDb.txt\n", $asmId, $asmId; printf "groups groups.txt\n"; printf "description %s\n", $orgName; printf "twoBitPath genomes/%s/%s.2bit\n", $asmId, $asmId; printf "organism %s\n", $descr; my $chrName=`head -1 $buildDir/$asmId.chrom.sizes | awk '{print \$1}'`; chomp $chrName; my $bigChrom=`head -1 $buildDir/$asmId.chrom.sizes | awk '{print \$NF}'`; chomp $bigChrom; my $oneThird = int($bigChrom/3); my $tenK = $oneThird + 10000; $tenK = $bigChrom if ($tenK > $bigChrom); my $defPos="${chrName}:${oneThird}-${tenK}"; if ( -s "$asmId/defaultPos.txt" ) { $defPos=`cat "$asmId/defaultPos.txt"`; chomp $defPos; } printf "defaultPos %s\n", $defPos; printf "orderKey %d\n", $orderKey++; printf "scientificName %s\n", $descr; printf "htmlPath genomes/%s/html/%s.description.html\n", $asmId, $asmId; printf "\n"; my $localGenomesFile = "$buildDir/${asmId}.genomes.txt"; open (GF, ">$localGenomesFile") or die "can not write to $localGenomesFile"; printf GF "genome %s\n", $asmId; - printf GF "trackDb %s/%s.trackDb.txt\n", $asmId, $asmId; - printf GF "groups groups.txt\n"; + printf GF "trackDb %s.trackDb.txt\n", $asmId; + printf GF "groups %s.groups.txt\n", $asmId; printf GF "description %s\n", $orgName; - printf GF "twoBitPath %s/%s.2bit\n", $asmId, $asmId; + printf GF "twoBitPath %s.2bit\n", $asmId; printf GF "organism %s\n", $descr; printf GF "defaultPos %s\n", $defPos; printf GF "orderKey %d\n", $orderKey++; printf GF "scientificName %s\n", $descr; - printf GF "htmlPath %s/html/%s.description.html\n", $asmId, $asmId; + printf GF "htmlPath html/%s.description.html\n", $asmId; close (GF); + my $localHubTxt = "$buildDir/${asmId}.hub.txt"; + open (HT, ">$localHubTxt") or die "can not write to $localHubTxt"; + printf HT "hub %s genome assembly\n", $asmId; + printf HT "shortLabel %s\n", $orgName; + printf HT "longLabel %s/%s/%s genome assembly\n", $orgName, $descr, $asmId; + printf HT "genomesFile %s.genomes.txt\n", $asmId; + printf HT "email hclawson\@ucsc.edu\n"; + printf HT "descriptionUrl html/%s.description.html\n", $asmId; + close (HT); + + my $localGroups = "$buildDir/${asmId}.groups.txt"; + open (GR, ">$localGroups") or die "can not write to $localGroups"; + print GR <<_EOF_ +name user +label Custom +priority 1 +defaultIsClosed 1 + +name map +label Mapping +priority 2 +defaultIsClosed 0 + +name genes +label Genes +priority 3 +defaultIsClosed 0 + +name rna +label mRNA +priority 4 +defaultIsClosed 0 + +name regulation +label Regulation +priority 5 +defaultIsClosed 0 + +name compGeno +label Comparative +priority 6 +defaultIsClosed 0 + +name varRep +label Variation +priority 7 +defaultIsClosed 0 + +name x +label Experimental +priority 10 +defaultIsClosed 1 +_EOF_ + ; + close (GR); } __END__ description Mastacembelus armatus twoBitPath GCA_900324485.2_fMasArm1.2/trackData/addMask/GCA_900324485.2_fMasArm1.2.masked.2bit organism Zig-Zag eel defaultPos LR535842.1:14552035-14572034 orderKey 1 scientificName Mastacembelus armatus htmlPath GCA_900324485.2_fMasArm1.2/html/GCA_900324485.2_fMasArm1.2.description.html # head -25 GCA_002180035.3_HG00514_prelim_3.0_assembly_report.txt # Assembly name: HG00514_prelim_3.0 # Organism name: Homo sapiens (human) # Isolate: HG00514 # Sex: female # Taxid: 9606 # BioSample: SAMN04229552 # BioProject: PRJNA300843 # Submitter: The Genome Institute at Washington University School of Medicine # Date: 2018-05-22 # Assembly type: haploid # Release type: major # Assembly level: Chromosome # Genome representation: full # WGS project: NIOH01 # Assembly method: Falcon v. November 2016 # Expected final version: no # Genome coverage: 80.0x # Sequencing technology: PacBio RSII # GenBank assembly accession: GCA_002180035.3 # ## Assembly-Units: ## GenBank Unit Accession RefSeq Unit Accession Assembly-Unit name ## GCA_002180045.3 Primary Assembly