27228c7e494674469a64cdeb61d7c4e433102f24 hiram Thu Jan 2 13:16:14 2020 -0800 updated text to global reference wording refs #24534 diff --git src/hg/makeDb/doc/globalReference/mkHubIndex.pl src/hg/makeDb/doc/globalReference/mkHubIndex.pl index 52db04b..60b8cc4 100755 --- src/hg/makeDb/doc/globalReference/mkHubIndex.pl +++ src/hg/makeDb/doc/globalReference/mkHubIndex.pl @@ -1,254 +1,256 @@ #!/usr/bin/env perl use strict; use warnings; my $Name = "GlobalReference"; my $asmHubWorkDir = "globalReference"; 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 $timeStamp; # <html xmlns="http://www.w3.org/1999/xhtml"> print <<"END" <!DOCTYPE HTML 4.01 Transitional> -<!--#set var="TITLE" value="Platinum Genomes Project assembly hub" --> +<!--#set var="TITLE" value="Global Reference Genomes assembly hubs" --> <!--#set var="ROOT" value="../.." --> <!--#include virtual="\$ROOT/inc/gbPageStartHardcoded.html" --> -<h1>Platinum Genomes Project assembly hub</h1> +<h1>Global Reference Genomes assembly hubs</h1> <p> -This assembly hub contains assemblies released -by the <a href='https://genome.cshlp.org/content/27/1/157' target=_blank> -Platinum Genomes Project.</a> +This assembly hub contains ten high-quality, population-identified assemblies released +by the <a href='https://www.genome.wustl.edu/items/reference-genome-improvement/' target=_blank> +Reference Genome Improvement</a> project. This population list is not conclusive and +represents reference genomes from 10 different human populations. Thank you to +Washington University in Saint Louis for consolidating these open source reference genomes. </p> <h3>How to view the hub</h3> <p> You can load this hub from our <a href="https://genome.ucsc.edu/cgi-bin/hgHubConnect#publicHubs" target="_blank">Public Hubs</a> -page or by clicking these links to any of our official websites: +page or by clicking these assembly links to any of our official websites: <ul> <li> <a href="https://genome.ucsc.edu/cgi-bin/hgGateway?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/$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. +genome assemblies can be selected from the <em>Reference Genome Improvement Hub Assembly</em> dropdown menu. </p> <p> <h3>See also: <a href='asmStats$Name.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/$asmHubWorkDir"; open (FH, "<$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();