be4311c07e14feb728abc6425ee606ffaa611a58
markd
  Fri Jan 22 06:46:58 2021 -0800
merge with master

diff --git src/hg/utils/automation/asmHubGatewayPage.pl src/hg/utils/automation/asmHubGatewayPage.pl
index 5024ee8..07b361e 100755
--- src/hg/utils/automation/asmHubGatewayPage.pl
+++ src/hg/utils/automation/asmHubGatewayPage.pl
@@ -1,439 +1,439 @@
 #!/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 @months = qw( 0 Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec );
 
 sub usage() {
   printf STDERR "usage: asmHubGatewayPage.pl <asmHubName> <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 ) {
     printf STDERR "# reading chrom.sizes file:\n#\t'%s\'\n", $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;
 
     my $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 != 5) {
   usage;
 }
 
 my ($asmHubName, $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 $photoCreditURL = "";
 my $photoCreditName = "";
 my $imageSize = "";
 my $imageName = "";
 my $imageWidth = 0;
 my $imageHeight = 0;
 my $imageWidthBorder = 15;
 
 if ($jpgImage ne "noPhoto") {
   printf STDERR "# reading $photoCredits\n";
   open (FH, "<$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 $asmId = basename($ftpName);;
 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 $speciesSubgroup = $ftpName;
 my $asmType = "genbank";
-$asmType = "refseq" if ( $speciesSubgroup =~ m#refseq/#);
+$asmType = "refseq" if ( $gcXPrefix =~ m#GCF#);
 $speciesSubgroup =~ s#genomes/$asmType/##;;
 $speciesSubgroup =~ s#/.*##;;
 
 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;
 
 # printf "<script type='text/javascript'>var asmId='%s';</script>\n", $asmId;
 
 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>Common name:</b>&nbsp;%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=\"ftp://ftp.ncbi.nlm.nih.gov/genomes/all/%s\" target=\"_blank\">%s</a><br>
 \n", $commonName, $orgName, $taxId, $taxId, $submitter, $asmDate, $descrAsmType,
   $asmLevel, $bioSample, $bioSample, $asmAccession, $asmAccession, $newStyleUrl, $newStyleUrl;
 
 chromSizes($chromSizes);
 
 printf "</p>\n<hr>
 <p>
 <b>Download files for this assembly hub:</b><br>
 To use the data from this assembly for a local hub instance at your
 institution, download these data as indicated by these instructions.<br>
 <br>
 To download this assembly data, use this <em>rsync</em> command:
 <pre>
   rsync -a -P \\
     rsync://$sourceServer/hubs/$localDataUrl/ \\
       ./$accessionId/
 
   which creates the local directory: ./$accessionId/
 </pre>
 or this <em>wget</em> command:
 <pre>
   wget --timestamping -m -nH -x --cut-dirs=6 -e robots=off -np -k \\
     --reject \"index.html*\" -P \"$accessionId\" \\
        https://$sourceServer/hubs/$localDataUrl/
 
   which creates a local directory: ./$accessionId/
 </pre>
 <p>
 There is an included <em>hub.txt</em> file in that download
 data directory to use for your local track hub instance.<br>
 Using the genome browser menus: <em><strong>My Data</strong> -&gt; <strong>Track Hubs</strong></em><br>
 select the <em><strong>My Hubs</strong></em> tab to enter a URL
 to this hub.txt file to attach this assembly hub to a genome browser.
 </p>
 <p>
 The <em>html/$asmId.description.html</em> page is information for your users to
 describe this assembly.  This WEB page with these instructions
 is an instance of html/$asmId.description.html file.
 </p>
 <p>
 See also: <a href='/goldenPath/help/hgTrackHubHelp.html' target=_blank>track hub help</a> documentation.<br>
 </p>\n";
 
 printf "<hr>
 <p>
 To operate a blat server on this assembly, in the directory where you have
 the <em>$asmId.2bit</em> file:
 <pre>
 gfServer -log=$asmId.gfServer.trans.log -ipLog -canStop start \\
     yourserver.domain.edu 76543 -trans -mask $asmId.2bit &
 gfServer -log=$asmId.gfServer.log -ipLog -canStop start \\
     yourserver.domain.edu 76542 -stepSize=5 $asmId.2bit &
 </pre>
 Adjust the port numbers <em>76543</em> <em>76542</em> and the
 <em>yourserver.domain.edu</em> for your local circumstances.<br>
 Typically, port numbers in the range <em>49152</em> to <em>65535</em>
 are available for private use as in this case.
 See also: <a href='https://www.iana.org/assignments/service-names-port-numbers/service-names-port-numbers.xhtml' target=_blank>IANA.org</a> port registry.
 </p>
 <p>
 Enter the following specifications in your <em>genomes.txt</em> file:
 <pre>
 transBlat yourserver.domain.edu 76543
 blat yourserver.domain.edu 76542
 </pre>
 See also: <a href=\"https://genome.ucsc.edu/goldenPath/help/hubQuickStartAssembly.html#blat\"
 target=_blank>Blat for an Assembly Hub</a>
 </p>\n";
 
 printf "<hr>
 <p>
 <b>Search the assembly:</b>
 <ul>
 <li>
 <b>By position or search term: </b> Use the &quot;position or search term&quot;
 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 &quot;search term&quot; box,
 choose your gene from the drop-down list, then press &quot;submit&quot; to go
 directly to the assembly location associated with that gene.
 <a href=\"http://genome.ucsc.edu/goldenPath/help/geneSearchBox.html\">More information</a>.</li>
 <li>
 <b>By track type: </b> Click the &quot;track search&quot; 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";
 
 # printf "<script type='text/javascript' src='../js/gatewayPage.js'></script>\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