68e60a3ccfe0c3aaa48f2fa85f86ca700d681e81 hiram Tue Mar 31 12:08:22 2020 -0700 correct hub.txt not testHub.txt refs #23891 diff --git src/hg/makeDb/doc/asmHubs/mkHubIndex.pl src/hg/makeDb/doc/asmHubs/mkHubIndex.pl index d21d570..9402773 100755 --- src/hg/makeDb/doc/asmHubs/mkHubIndex.pl +++ src/hg/makeDb/doc/asmHubs/mkHubIndex.pl @@ -1,286 +1,293 @@ #!/usr/bin/env perl use strict; use warnings; my $argc = scalar(@ARGV); if ($argc != 3) { printf STDERR "mkAsmStats Name asmName\n"; printf STDERR "e.g.: mkHubIndex Primates primates GCF_000001405.39_GRCh38.p13\n"; exit 255; } my $Name = shift; my $asmHubName = shift; my $defaultAssembly = shift; my $home = $ENV{'HOME'}; my $toolsDir = "$home/kent/src/hg/makeDb/doc/asmHubs"; 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 $assemblyCount = 0; my %betterName; # key is asmId, value is a common name better than found # in assembly_report file ############################################################################## # from Perl Cookbook Recipe 2.17, print out large numbers with comma delimiters: ############################################################################## sub commify($) { 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"> my $subSetMessage = "subset of $asmHubName only"; if ($asmHubName eq "vertebrate") { $subSetMessage = "subset of other ${asmHubName}s only"; } print <<"END" <!DOCTYPE HTML 4.01 Transitional> <!--#set var="TITLE" value="$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, $subSetMessage. </p> <h3>How to view the hub</h3> <p> -You can load this hub from our -<a href="https://genome.ucsc.edu/cgi-bin/hgHubConnect#publicHubs" target="_blank">Public Hubs</a> -page or by clicking these assembly links to any of our official websites: +Options: +<ol> + <li>The links to the genome browser in the table below will attach that + one specific assembly to the genome browser. This is most likely what + you want.</li> + <li>Instead, you can attach the entire set of assemblies as one group to + the genome browser with the following links depending upon which of + our mirror site browsers you prefer to use: <ul> - <li> - <a href="https://genome.ucsc.edu/cgi-bin/hgGateway?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/$asmHubName/hub.txt&genome=$defaultAssembly" + <li><a href="https://genome.ucsc.edu/cgi-bin/hgGateway?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/$asmHubName/hub.txt&genome=GCF_000001405.39" 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" + <li><a href="https://genome-euro.ucsc.edu/cgi-bin/hgGateway?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/$asmHubName/hub.txt&genome=GCF_000001405.39" target="_blank">genome-euro.ucsc.edu</a></li> - <li> - <a href="https://genome-asia.ucsc.edu/cgi-bin/hgGateway?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/$asmHubName/hub.txt&genome=$defaultAssembly" + <li><a href="https://genome-asia.ucsc.edu/cgi-bin/hgGateway?hubUrl=https://hgdownload.soe.ucsc.edu/hubs/$asmHubName/hub.txt&genome=GCF_000001405.39" target="_blank">genome-asia.ucsc.edu</a></li> </ul> -</p> - -<p> -To manually attach all the assemblies in this hub to other genome browsers: + </li> + <li>To manually attach all the assemblies in this hub to genome browsers + that are not one of the three UCSC mirror sites: <ol> - <li> - From the blue navigation bar, go to + <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: + <li>Then select the <strong>My Hubs</strong> tab and enter this URL into + the textbox: <br><code>https://hgdownload.soe.ucsc.edu/hubs/$asmHubName/hub.txt</code></li> - <li> - Once you have added the URL to the entry form, press the <em><strong>Add Hub</strong></em> - button to add the hub.</li> + <li> Once you have added the URL to the entry form, + press the <em><strong>Add Hub</strong></em> button to add the hub.</li> + </ol> + </li> </ol> </p> <p> After adding the hub, you will be redirected to the gateway page. The genome assemblies can be selected from the <em>${Name} 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${Name}.html'>assembly statistics</a>, <a href='trackData.html'>track statistics</a></h3><br> +<h3>See also: <a href='asmStats.html'>assembly statistics</a>, <a href='trackData.html'>track statistics</a> <== additional information for these assemblies.</h3><br> <h3>Data resource links</h3> +<p> NOTE: <em>Click on the column headers to sort the table by that column</em><br> -The <em>link to genome browser</em> will attach only that single assembly to -the genome browser. +The <em>common name/link to genome browser</em> will attach only that single assembly to +the genome browser.<br> +The <em>scientific name/and data download</em> link provides access to the files for that one +assembly hub.<br> +The other links provide access to NCBI resources for these assemblies. +</p> END } # sub startHtml() ############################################################################## ### start the table output ############################################################################## sub startTable() { print <<"END" <table class="sortable" border="1"> <thead><tr><th>count</th> <th>common name<br>link to genome browser</th> <th>scientific name<br>and data download</th> <th>NCBI assembly</th> <th>bioSample</th><th>bioProject</th> <th>assembly date,<br>source link</th> </tr></thead><tbody> END } # sub startTable() ############################################################################## ### end the table output ############################################################################## sub endTable() { print <<"END" </tbody> </table> END } # sub endTable() ############################################################################## ### end the HTML output ############################################################################## sub endHtml() { if ($asmHubName ne "viral") { - printf "<p>\n<table border='1'><thead>\n<tr>"; - printf "<th>Assembly hubs index pages: </th>\n"; + printf "<p>\n<table border='1'><thead>\n"; + printf "<tr><th colspan=6 style='text-align:center;'>Additional hubs with collections of assemblies</th></tr>\n"; + printf "<tr><th>Assembly hubs index pages: </th>\n"; printf "<th><a href='../primates/index.html'>Primates</a></th>\n"; printf "<th><a href='../mammals/index.html'>Mammals</a></th>\n"; printf "<th><a href='../birds/index.html'>Birds</a></th>\n"; printf "<th><a href='../fish/index.html'>Fish</a></th>\n"; printf "<th><a href='../vertebrate/index.html'>other vertebrates</a></th>\n"; printf "</tr><tr>\n"; printf "<th>Hubs assembly statistics: </th>\n"; - printf "<th><a href='../primates/asmStatsPrimates.html'>Primates</a></th>\n"; - printf "<th><a href='../mammals/asmStatsMammals.html'>Mammals</a></th>\n"; - printf "<th><a href='../birds/asmStatsBirds.html'>Birds</a></th>\n"; - printf "<th><a href='../fish/asmStatsFish.html'>Fish</a></th>\n"; - printf "<th><a href='../vertebrate/asmStatsVertebrate.html'>other vertebrates</a></th>\n"; + printf "<th><a href='../primates/asmStats.html'>Primates</a></th>\n"; + printf "<th><a href='../mammals/asmStats.html'>Mammals</a></th>\n"; + printf "<th><a href='../birds/asmStats.html'>Birds</a></th>\n"; + printf "<th><a href='../fish/asmStats.html'>Fish</a></th>\n"; + printf "<th><a href='../vertebrate/asmStats.html'>other vertebrates</a></th>\n"; printf "</tr><tr>\n"; printf "<th>Hubs track statistics: </th>\n"; printf "<th><a href='../primates/trackData.html'>Primates</a></th>\n"; printf "<th><a href='../mammals/trackData.html'>Mammals</a></th>\n"; printf "<th><a href='../birds/trackData.html'>Birds</a></th>\n"; printf "<th><a href='../fish/trackData.html'>Fish</a></th>\n"; printf "<th><a href='../vertebrate/trackData.html'>other vertebrates</a></th>\n"; printf "</tr></thead>\n</table>\n</p>\n"; } 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 $asmId (reverse(@orderList)) { my ($gcPrefix, $asmAcc, $asmName) = split('_', $asmId, 3); my $accessionId = sprintf("%s_%s", $gcPrefix, $asmAcc); my $accessionDir = substr($asmId, 0 ,3); $accessionDir .= "/" . substr($asmId, 4 ,3); $accessionDir .= "/" . substr($asmId, 7 ,3); $accessionDir .= "/" . substr($asmId, 10 ,3); my $ncbiFtpLink = "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/$accessionDir/$asmId"; my $buildDir = "/hive/data/genomes/asmHubs/refseqBuild/$accessionDir/$asmId"; my $asmReport="$buildDir/download/${asmId}_assembly_report.txt"; my $trackDb="$buildDir/${asmId}.trackDb.txt"; next if (! -s "$trackDb"); 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/.*\(//; $commonName =~ s/\)//; $commonName = $betterName{$asmId} if (exists($betterName{$asmId})); $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/$accessionId"; printf "<tr><td align=right>%d</td>\n", ++$rowCount; ### printf "<td align=center><a href='https://genome.ucsc.edu/cgi-bin/hgGateway?hubUrl=%s/hub.txt&genome=%s&position=lastDbPos' target=_blank>%s</a></td>\n", $hubUrl, $accessionId, $commonName; printf "<td align=center><a href='https://genome.ucsc.edu/h/%s' target=_blank>%s</a></td>\n", $accessionId, $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, $asmDate; printf "</tr>\n"; } } # sub tableContents() ############################################################################## ### main() ############################################################################## open (FH, "<$toolsDir/${commonNameOrder}") or die "can not read ${commonNameOrder}"; while (my $line = <FH>) { next if ($line =~ m/^#/); chomp $line; my ($commonName, $asmId) = split('\t', $line); push @orderList, $asmId; $betterName{$asmId} = $commonName; ++$assemblyCount; } close (FH); startHtml(); startTable(); tableContents(); endTable(); endHtml();