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/mkHubIndex.pl src/hg/makeDb/doc/vertebratesAsmHub/mkHubIndex.pl new file mode 100755 index 0000000..f598eb4 --- /dev/null +++ src/hg/makeDb/doc/vertebratesAsmHub/mkHubIndex.pl @@ -0,0 +1,241 @@ +#!/usr/bin/env perl + +use strict; +use warnings; + +my $home = $ENV{'HOME'}; +my $Name = "Vertebrate"; +my $asmHubName = "vertebrate"; +my $srcDocDir = "${asmHubName}sAsmHub"; +my $asmHubDocDir = "$home/kent/src/hg/makeDb/doc/$srcDocDir"; +my $defaultAssembly = "GCF_000281125.3_ASM28112v4"; # Alligator_mississippiensis + +my $srcDir = "$home/kent/src/hg/makeDb/doc/$srcDocDir"; +my $commonNameOrder = "$asmHubName.commonName.asmId.orderList.tsv"; + +my @orderList; # asmId of the assemblies in order from the *.list files +# the order to read the different .list files: +my $assemblyCount = 0; + +############################################################################## +# from Perl Cookbook Recipe 2.17, print out large numbers with comma delimiters: +############################################################################## +sub commify($) { + my $text = reverse $_[0]; + $text =~ s/(\d\d\d)(?=\d)(?!\d*\.)/$1,/g; + return scalar reverse $text +} + +############################################################################## +### start the HTML output +############################################################################## +sub startHtml() { + +my $timeStamp = `date "+%F"`; +chomp $timeStamp; + +# <html xmlns="http://www.w3.org/1999/xhtml"> + +print <<"END" +<!DOCTYPE HTML 4.01 Transitional> +<!--#set var="TITLE" value="$Name genomes assembly hubs" --> +<!--#set var="ROOT" value="../.." --> + +<!--#include virtual="\$ROOT/inc/gbPageStartHardcoded.html" --> + +<h1>$Name Genomes assembly hubs</h1> +<p> +Assemblies from NCBI/Genbank/Refseq sources, subset of other ${asmHubName}s only. +</p> + +<h3>How to view the hub</h3> +<p> +You can load this hub from our +<a href="https://genome.ucsc.edu/cgi-bin/hgHubConnect#publicHubs" target="_blank">Public Hubs</a> +page or by clicking these assembly links to any of our official websites: +<ul> + <li> + <a href="https://genome.ucsc.edu/cgi-bin/hgGateway?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/$asmHubName/hub.txt&genome=$defaultAssembly" + target="_blank">genome.ucsc.edu</a></li> + <li> + <a href="https://genome-euro.ucsc.edu/cgi-bin/hgGateway?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/$asmHubName/hub.txt&genome=$defaultAssembly" + target="_blank">genome-euro.ucsc.edu</a></li> + <li> + <a href="https://genome-asia.ucsc.edu/cgi-bin/hgGateway?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/$asmHubName/hub.txt&genome=$defaultAssembly" + target="_blank">genome-asia.ucsc.edu</a></li> +</ul> +</p> + +<p> +To manually attach all the assemblies in this hub to other genome browsers: +<ol> + <li> + From the blue navigation bar, go to + <em><strong>My Data</strong> -> <strong>Track Hubs</strong></em></li> + <li> + Then select the <strong>My Hubs</strong> tab and enter this URL into the textbox: + <br><code>https://hgdownload.soe.ucsc.edu/hubs/$asmHubName/hub.txt</code></li> + <li> + Once you have added the URL to the entry form, press the <em><strong>Add Hub</strong></em> + button to add the hub.</li> +</ol> +</p> + +<p> +After adding the hub, you will be redirected to the gateway page. The +genome assemblies can be selected from the +<em>${Name}s Hub Assembly</em> dropdown menu. +Instead of adding all the assemblies in one collected group, use the individual +<em>link to genome browser</em> in the table below. +</p> +<h3>See also: <a href='asmStats$Name.html' +target=_blank>assembly statistics</a></h3><br> +<h3>Data resource links</h3> +NOTE: <em>Click on the column headers to sort the table by that column</em><br> +The <em>link to genome browser</em> will attach only that single assembly to +the genome browser. +END +} # sub startHtml() + +############################################################################## +### start the table output +############################################################################## +sub startTable() { +print <<"END" +<table class="sortable" border="1"> +<thead><tr><th>count</th> + <th>common name<br>link to genome browser</th> + <th>scientific name<br>and data download</th> + <th>NCBI assembly</th> + <th>bioSample</th><th>bioProject</th> + <th>assembly date,<br>source link</th> +</tr></thead><tbody> +END +} # sub startTable() + +############################################################################## +### end the table output +############################################################################## +sub endTable() { + +print <<"END" + +</tbody> +</table> +END +} # sub endTable() + +############################################################################## +### end the HTML output +############################################################################## +sub endHtml() { +print <<"END" +</div><!-- closing gbsPage from gbPageStartHardcoded.html --> +</div><!-- closing container-fluid from gbPageStartHardcoded.html --> +<!--#include virtual="\$ROOT/inc/gbFooterHardcoded.html"--> +<script type="text/javascript" src="/js/sorttable.js"></script> +</body></html> +END +} # sub endHtml() + +############################################################################## +### tableContents() +############################################################################## +sub tableContents() { + my $rowCount = 0; + foreach my $asmId (@orderList) { + my $accessionDir = substr($asmId, 0 ,3); + $accessionDir .= "/" . substr($asmId, 4 ,3); + $accessionDir .= "/" . substr($asmId, 7 ,3); + $accessionDir .= "/" . substr($asmId, 10 ,3); + $accessionDir .= "/" . $asmId; + my $ncbiFtpLink = "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/$accessionDir/"; + my $buildDir = "/hive/data/genomes/asmHubs/refseqBuild/$accessionDir"; + my $asmReport="$buildDir/download/${asmId}_assembly_report.txt"; + my ($gcPrefix, $asmAcc, $asmName) = split('_', $asmId, 3); + my $chromSizes="${buildDir}/${asmId}.chrom.sizes"; + my $sciName = "notFound"; + my $commonName = "notFound"; + my $bioSample = "notFound"; + my $bioProject = "notFound"; + my $taxId = "notFound"; + my $asmDate = "notFound"; + my $itemsFound = 0; + open (FH, "<$asmReport") or die "can not read $asmReport"; + while (my $line = <FH>) { + last if ($itemsFound > 5); + chomp $line; + $line =~ s/ //g;; + $line =~ s/\s+$//g;; + if ($line =~ m/Date:/) { + if ($asmDate =~ m/notFound/) { + ++$itemsFound; + $line =~ s/.*:\s+//; + my @a = split('-', $line); + $asmDate = sprintf("%04d-%02d-%02d", $a[0], $a[1], $a[2]); + } + } elsif ($line =~ m/BioSample:/) { + if ($bioSample =~ m/notFound/) { + ++$itemsFound; + $bioSample = $line; + $bioSample =~ s/.*:\s+//; + } + } elsif ($line =~ m/BioProject:/) { + if ($bioProject =~ m/notFound/) { + ++$itemsFound; + $bioProject = $line; + $bioProject =~ s/.*:\s+//; + } + } elsif ($line =~ m/Organism name:/) { + if ($sciName =~ m/notFound/) { + ++$itemsFound; + $commonName = $line; + $sciName = $line; + $commonName =~ s/.*\(//; + $commonName =~ s/\)//; + $sciName =~ s/.*:\s+//; + $sciName =~ s/\s+\(.*//; + } + } elsif ($line =~ m/Taxid:/) { + if ($taxId =~ m/notFound/) { + ++$itemsFound; + $taxId = $line; + $taxId =~ s/.*:\s+//; + } + } + } + close (FH); + my $hubUrl = "https://hgdownload.soe.ucsc.edu/hubs/$accessionDir"; + printf "<tr><td align=right>%d</td>\n", ++$rowCount; + printf "<td align=center><a href='https://genome.ucsc.edu/cgi-bin/hgGateway?hubUrl=%s/%s.hub.txt&genome=%s&position=lastDbPos' target=_blank>%s</a></td>\n", $hubUrl, $asmId, $asmId, $commonName; + printf " <td align=center><a href='%s/' target=_blank>%s</a></td>\n", $hubUrl, $sciName; + printf " <td align=left><a href='https://www.ncbi.nlm.nih.gov/assembly/%s_%s/' target=_blank>%s</a></td>\n", $gcPrefix, $asmAcc, $asmId; + if ( $bioSample ne "notFound" ) { + printf " <td align=left><a href='https://www.ncbi.nlm.nih.gov/biosample/?term=%s' target=_blank>%s</a></td>\n", $bioSample, $bioSample; + } else { + printf " <td align=left>n/a</td>\n"; + } + printf " <td align=left><a href='https://www.ncbi.nlm.nih.gov/bioproject/?term=%s' target=_blank>%s</a></td>\n", $bioProject, $bioProject; + printf " <td align=center><a href='%s' target=_blank>%s</a></td>\n", $ncbiFtpLink, $asmDate; + printf "</tr>\n"; + } +} # sub tableContents() + +############################################################################## +### main() +############################################################################## + +open (FH, "<$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); + +startHtml(); +startTable(); +tableContents(); +endTable(); +endHtml();