10a6e5cd8350a3409c7a053ac6f78be70f459c2c hiram Mon Oct 7 14:20:32 2019 -0700 files to build the platinum genomes assembly hub refs #21784 diff --git src/hg/makeDb/doc/platinum/mkHubIndex.pl src/hg/makeDb/doc/platinum/mkHubIndex.pl new file mode 100755 index 0000000..aa5ae8b --- /dev/null +++ src/hg/makeDb/doc/platinum/mkHubIndex.pl @@ -0,0 +1,253 @@ +#!/usr/bin/env perl + +use strict; +use warnings; + +my $asmHubWorkDir = "platinum"; +my $defaultAssembly = "GCA_001524155.4_NA19240_prelim_3.0"; + +my @orderList; # asmId of the assemblies in order from the *.list files +# the order to read the different .list files: +my @classList = qw( human ); +my %class; # key is asmId, value is from class list +my $assemblyCount = 0; + +my %coriellLink; # key is asmId, value is isolate ID to construct link +# https://www.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=<isolateId> +my %ethnicGroup; # ksy is asmId, value is ethnicity +my %countryOfOrigin; # ksy is asmId, value is country of origin + +############################################################################## +# from Perl Cookbook Recipe 2.17, print out large numbers with comma delimiters: +############################################################################## +sub commify($) { + 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 $timeStamp; + +# <html xmlns="http://www.w3.org/1999/xhtml"> + +print <<"END" +<!DOCTYPE HTML 4.01 Transitional> +<!--#set var="TITLE" value="Platinum Genomes Project assembly hub" --> +<!--#set var="ROOT" value="../.." --> + +<!--#include virtual="\$ROOT/inc/gbPageStartHardcoded.html" --> + +<h1>Platinum Genomes Project assembly hub</h1> +<p> +This assembly hub contains assemblies released +by the <a href='https://genome.cshlp.org/content/27/1/157' target=_blank> +Platinum Genomes Project.</a> +</p> + +<h3>How to view the hub</h3> +<p> +You can load this hub from our +<a href="https://genome.ucsc.edu/cgi-bin/hgHubConnect#publicHubs" target="_blank">Public Hubs</a> +page or by clicking these links to any of our official websites: +<ul> + <li> + <a href="https://genome.ucsc.edu/cgi-bin/hgGateway?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/$asmHubWorkDir/hub.txt&genome=$defaultAssembly" + target="_blank">genome.ucsc.edu</a></li> + <li> + <a href="https://genome-euro.ucsc.edu/cgi-bin/hgGateway?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/$asmHubWorkDir/hub.txt&genome=$defaultAssembly" + target="_blank">genome-euro.ucsc.edu</a></li> + <li> + <a href="https://genome-asia.ucsc.edu/cgi-bin/hgGateway?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/$asmHubWorkDir/hub.txt&genome=$defaultAssembly" + target="_blank">genome-asia.ucsc.edu</a></li> +</ul> +</p> + +<p> +To manually attach this hub to other genome browsers: +<ol> + <li> + From the blue navigation bar, go to + <em><strong>My Data</strong> -> <strong>Track Hubs</strong></em></li> + <li> + Then select the <strong>My Hubs</strong> tab and enter this URL into the textbox: + <br><code>https://hgdownload.soe.ucsc.edu/hubs/$asmHubWorkDir/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>Platinum Genomes Hub Assembly</em> dropdown menu. +</p> +<p> +<h3>See also: <a href='asmStatsPlatinum.html' target=_blank>assembly statistics</a></h3> +</p> +<h3>Data resource links</h3> +NOTE: <em>Click on the column headers to sort the table by that column</em> +END +} + +############################################################################## +### start the table output +############################################################################## +sub startTable() { +print <<"END" +<table class="sortable" border="1"> +<thead><tr><th>ethnicity<br>link to genome browser</th> + <th>country of origin<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 +} + +############################################################################## +### end the table output +############################################################################## +sub endTable() { + +print <<"END" + +</tbody> +</table> +END +} + +############################################################################## +### 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 +} + +############################################################################## +### tableContents() +############################################################################## +sub tableContents() { + open (CN, "|sort --ignore-case >commonNameOrder.list") or die "can not write to commonNameOrder.list"; + + foreach my $asmId (@orderList) { +# next if ($asmId =~ m/GCF_900963305.1_fEcheNa1.1/); + my $asmReport="${asmId}/download/${asmId}_assembly_report.txt"; + my ($gcPrefix, $asmAcc, $asmName) = split('_', $asmId, 3); + my $chromSizes="${asmId}/${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); + printf CN "%s\t%s\n", $commonName, $asmId; + printf "<tr><td align=center><a href='https://genome.ucsc.edu/cgi-bin/hgGateway?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/%s/hub.txt&genome=%s&position=lastDbPos' target=_blank>%s</a></td>\n", $asmHubWorkDir, $asmId, $ethnicGroup{$asmId}; + printf " <td align=center><a href='https://hgdownload.soe.ucsc.edu/hubs/%s/genomes/%s/' target=_blank>%s</a></td>\n", $asmHubWorkDir, $asmId, $countryOfOrigin{$asmId}; + printf " <td align=left><a href='https://www.ncbi.nlm.nih.gov/assembly/%s_%s/' target=_blank>%s</a></td>\n", $gcPrefix, $asmAcc, $asmId; + printf " <td align=left><a href='https://www.ncbi.nlm.nih.gov/biosample/?term=%s' target=_blank>%s</a></td>\n", $bioSample, $bioSample; + 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='https://www.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=%s' target=_blank>%s</a></td>\n", $coriellLink{$asmId}, $asmDate; + printf "</tr>\n"; + } + close(CN); +} + +############################################################################## +### main() +############################################################################## + +my $home = $ENV{'HOME'}; +my $srcDir = "$home/kent/src/hg/makeDb/doc/platinum"; + +open (FH, "<$srcDir/isolate.txt") or die "can not read $srcDir/isolate.txt"; +while (my $line = <FH>) { + chomp $line; + my ($asmId, $isolate) = split('\t', $line); + $coriellLink{$asmId} = $isolate; +} +close (FH); + +open (FH, "<$srcDir/ethnicGroup.txt") or die "can not read $srcDir/ethnicGroup.txt"; +while (my $line = <FH>) { + chomp $line; + my ($asmId, $ethnicGroup) = split('\t', $line); + my ($ethnic, $origin) = split(', ', $ethnicGroup); + $ethnicGroup{$asmId} = $ethnic; + $countryOfOrigin{$asmId} = $origin; +} +close (FH); + +foreach my $species (@classList) { + my $listFile = "$srcDir/${species}.list"; + open (FH, "<$listFile") or die "can not read $listFile"; + while (my $asmId = <FH>) { + chomp $asmId; + push @orderList, $asmId; + $class{$asmId} = $species; + ++$assemblyCount; + } + close (FH); +} + +startHtml(); +startTable(); +tableContents(); +endTable(); +endHtml();