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/mkSymLinks.pl src/hg/makeDb/doc/vertebratesAsmHub/mkSymLinks.pl
new file mode 100755
index 0000000..1cfb44d
--- /dev/null
+++ src/hg/makeDb/doc/vertebratesAsmHub/mkSymLinks.pl
@@ -0,0 +1,180 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+use File::Basename;
+
+my $topLevel = "/hive/data/genomes/asmHubs";
+
+my %betterName; # key is asmId, value is common name
+my $hubName = "vertebrate";
+my $Name = "Vertebrate";
+my $srcDocDir = "${hubName}sAsmHub";
+
+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 $destDir = "/hive/data/genomes/asmHubs";
+
+my $orderKey = 1;
+foreach my $asmId (reverse(@orderList)) {
+ my $accessionDir = substr($asmId, 0 ,3);
+ $accessionDir .= "/" . substr($asmId, 4 ,3);
+ $accessionDir .= "/" . substr($asmId, 7 ,3);
+ $accessionDir .= "/" . substr($asmId, 10 ,3);
+ $accessionDir .= "/" . $asmId;
+ $destDir = "/hive/data/genomes/asmHubs/$accessionDir";
+ my $buildDir = "/hive/data/genomes/asmHubs/refseqBuild/$accessionDir";
+ if ( ! -d "${destDir}" ) {
+ `mkdir -p "${destDir}"`;
+ }
+ printf STDERR "ln -s '${buildDir}' '${destDir}'\n";
+ `rm -f "${destDir}/bbi"`;
+ `rm -f "${destDir}/ixIxx"`;
+ `rm -fr "${destDir}/html"`;
+ `mkdir -p "${destDir}/html"`;
+ `rm -f "${destDir}/${asmId}.2bit"`;
+ `rm -f "${destDir}/${asmId}.agp.gz"`;
+ `rm -f "${destDir}/${asmId}.chrom.sizes"`;
+ `rm -f "${destDir}/${asmId}_assembly_report.txt"`;
+ `rm -f "${destDir}/${asmId}.trackDb.txt"`;
+ `rm -f "${destDir}/${asmId}.genomes.txt"`;
+ `rm -f "${destDir}/${asmId}.hub.txt"`;
+ `rm -f "${destDir}/${asmId}.groups.txt"`;
+ `ln -s "${buildDir}/bbi" "${destDir}/bbi"`;
+ `ln -s "${buildDir}/ixIxx" "${destDir}/ixIxx"`;
+ `ln -s ${buildDir}/html/*.html "${destDir}/html/"`;
+ my $jpgFiles =`ls ${buildDir}/html/*.jpg 2> /dev/null | wc -l`;
+ chomp $jpgFiles;
+ if ($jpgFiles > 0) {
+ `rm -f ${destDir}/html/*.jpg`;
+ `ln -s ${buildDir}/html/*.jpg "${destDir}/html/"`;
+ }
+# `ln -s ${buildDir}/html/*.png "${destDir}/genomes/${asmId}/html/"`;
+ `ln -s "${buildDir}/${asmId}.2bit" "${destDir}/"`;
+ `ln -s "${buildDir}/${asmId}.agp.gz" "${destDir}/"`;
+ `ln -s "${buildDir}/${asmId}.chrom.sizes" "${destDir}/"`;
+ `ln -s "${buildDir}/download/${asmId}_assembly_report.txt" "${destDir}/"`;
+ `ln -s "${buildDir}/${asmId}.trackDb.txt" "${destDir}/"`;
+ `ln -s "${buildDir}/${asmId}.genomes.txt" "${destDir}/"`;
+ `ln -s "${buildDir}/${asmId}.hub.txt" "${destDir}/"`;
+ `ln -s "${buildDir}/${asmId}.groups.txt" "${destDir}/"`;
+}
+
+__END__
+
+my $hubDir = "/gbdb/hubs/$hubName";
+
+`rm -f "${hubDir}/index.html"`;
+`ln -s "${destDir}/index.html" "${hubDir}/index.html"`;
+`rm -f "${hubDir}/testIndex.html"`;
+`ln -s "${destDir}/testIndex.html" "${hubDir}/testIndex.html"`;
+`rm -f "${hubDir}/testAsmStats${Name}.html"`;
+`ln -s "${destDir}/testAsmStats${Name}.html" "${hubDir}/testAsmStats${Name}.html"`;
+
+__END__
+;
+ 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 "description %s\n", $orgName;
+ printf GF "twoBitPath %s/%s.2bit\n", $asmId, $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;
+ close (GF);
+}
+
+__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
+