9f30c7b8a1cc0c6b082f96b0ff1a2f2011a5992e lrnassar Fri Aug 2 09:15:01 2019 -0700 Fixing some links to look better #23734 diff --git src/hg/makeDb/doc/VGP/mkHubIndex.pl src/hg/makeDb/doc/VGP/mkHubIndex.pl index f93481a..98a4528 100755 --- src/hg/makeDb/doc/VGP/mkHubIndex.pl +++ src/hg/makeDb/doc/VGP/mkHubIndex.pl @@ -1,246 +1,246 @@ #!/usr/bin/env perl use strict; use warnings; my @orderList; # asmId of the assemblies in order from the *.list files # the order to read the different .list files: my @classList = qw( mammal bird reptile amphibian fish ); my %class; # key is asmId, value is from class list my $assemblyCount = 0; my %betterName; # key is asmId, value is common name ############################################################################## # from Perl Cookbook Recipe 2.17, print out large numbers with comma delimiters: ############################################################################## sub commify($) { 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="VGP - Vertebrate Genomes Project assembly hub - $timeStamp" --> <!--#set var="ROOT" value="../.." --> <!--#include virtual="\$ROOT/inc/gbPageStartHardcoded.html" --> <h1>VGP - Vertebrate Genomes Project assembly hub - $timeStamp</h1> <p> This assembly hub contains some of the first complete assemblies released by the <a href='https://vertebrategenomesproject.org/' target=_blank> Vertebrate Genomes Project.<br> <img src='VGPlogo.png' width=280 alt='VGP logo'></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="http://genome.ucsc.edu/cgi-bin/hgGateway?hubUrl=http://genome-test.gi.ucsc.edu/hubs/VGP/hub.txt&genome=GCF_004126475.1_mPhyDis1_v1.p" target="_blank">genome.ucsc.edu</a></li> <li> <a href="http://genome-euro.ucsc.edu/cgi-bin/hgGateway?hubUrl=http://genome-test.gi.ucsc.edu/hubs/VGP/hub.txt&genome=GCF_004126475.1_mPhyDis1_v1.p" target="_blank">genome-euro.ucsc.edu</a></li> <li> <a href="http://genome-asia.ucsc.edu/cgi-bin/hgGateway?hubUrl=http://genome-test.gi.ucsc.edu/hubs/VGP/hub.txt&genome=GCF_004126475.1_mPhyDis1_v1.p" 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>http://genome-test.gi.ucsc.edu/hubs/VGP/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>VGP Hub Assembly</em> dropdown menu. </p> <p> -<h3>See also: <a href='asmStatsVGP.html' target=_blank>assembly statistics</a> information</h3> +<h3>See also: <a href='asmStatsVGP.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>common name and<br>view in browser</th> <th>scientific name and<br>data download</th> <th>NCBI assembly</th> <th>bioSample</th><th>bioProject</th> <th>Taxon ID</th> <th>assembly date<br>VGP link</th> <th>class</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; $asmDate = $line; $asmDate =~ s/.*:\s+//; } } elsif ($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); $commonName = $betterName{$asmId} if (exists($betterName{$asmId})); printf CN "%s\t%s\n", $commonName, $asmId; printf "<tr><td align=center><a href='https://genome-test.gi.ucsc.edu/cgi-bin/hgGateway?hubUrl=http://genome-test.gi.ucsc.edu/hubs/VGP/hub.txt&genome=%s&position=lastDbPos' target=_blank>%s</a></td>\n", $asmId, $commonName; printf " <td align=center><a href='https://genome-test.gi.ucsc.edu/hubs/VGP/genomes/%s/' target=_blank>%s</a></td>\n", $asmId, $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; 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=right><a href='https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=%d' target=_blank>%s</a></td>\n", $taxId, $taxId; my $sciNameUnderscore = $sciName; $sciNameUnderscore =~ s/ /_/g; $sciNameUnderscore = "Strigops_habroptilus" if ($sciName =~ m/Strigops habroptila/); printf " <td align=center><a href='https://vgp.github.io/genomeark/%s/' target=_blank>%s</a></td>\n", $sciNameUnderscore, $asmDate; printf " <td align=right>%s</td>\n", $class{$asmId}; printf "</tr>\n"; } close(CN); } ############################################################################## ### main() ############################################################################## my $home = $ENV{'HOME'}; my $srcDir = "$home/kent/src/hg/makeDb/doc/VGP"; open (FH, "<$srcDir/commonNames.txt") or die "can not read $srcDir/commonNames.txt"; while (my $line = <FH>) { chomp $line; my ($asmId, $name) = split('\t', $line); $betterName{$asmId} = $name; } 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();