a7652d074beefd4f023287d09ec32bc2bbf43796 hiram Fri Jan 24 10:26:32 2020 -0800 now using common scripts to build hubs refs #24748 diff --git src/hg/makeDb/doc/primateAsmHub/mkHubIndex.pl src/hg/makeDb/doc/primateAsmHub/mkHubIndex.pl deleted file mode 100755 index f1528d3..0000000 --- src/hg/makeDb/doc/primateAsmHub/mkHubIndex.pl +++ /dev/null @@ -1,244 +0,0 @@ -#!/usr/bin/env perl - -use strict; -use warnings; - -my $home = $ENV{'HOME'}; -my $srcDocDir = "primateAsmHub"; -my $asmHubDocDir = "$home/kent/src/hg/makeDb/doc/$srcDocDir"; -my $Name = "Primate"; -my $asmHubName = "primates"; -my $defaultAssembly = "GCF_000001405.39_GRCh38.p13"; - -my $srcDir = "$home/kent/src/hg/makeDb/doc/$srcDocDir"; -my $commonNameOrder = "primates.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 $asmHubName only. -</p> - -<h3>How to view the hub</h3> -<p> -Individual assemblies are attached to the genome browser via the -<em>link to genome browser</em> in the table below. To attach all -of these assemblies in one set for this hub, select the ${Name}s assembly -hub from our -<a href="https://genome.ucsc.edu/cgi-bin/hgHubConnect#publicHubs" target="_blank">Public Hubs</a> -page or by clicking these assembly links to any of our official websites: -<ul> - <li> - <a href="https://genome.ucsc.edu/cgi-bin/hgGateway?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/$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();