f654134d5172e2687b3e6f98da7db78dd8379387 hiram Tue Jan 21 15:01:57 2020 -0800 initial set of files to build "other vertebrates" assembly hub refs #2482 diff --git src/hg/makeDb/doc/vertebratesAsmHub/mkGenomes.pl src/hg/makeDb/doc/vertebratesAsmHub/mkGenomes.pl new file mode 100755 index 0000000..ad51cf0 --- /dev/null +++ src/hg/makeDb/doc/vertebratesAsmHub/mkGenomes.pl @@ -0,0 +1,182 @@ +#!/usr/bin/env perl + +use strict; +use warnings; +use File::Basename; + +my %betterName; # key is asmId, value is common name +my $hubName = "vertebrate"; +my $srcDocDir = "vertebratesAsmHub"; +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 $commonNameList = "$hubName.asmId.commonName.tsv"; +my $commonNameOrder = "$hubName.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.trackDb.txt\n", $asmId; + printf GF "groups %s.groups.txt\n", $asmId; + printf GF "description %s\n", $orgName; + 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 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 +