790b166f17ba0ef2f8cfe220dbc6c2a67035ede9 hiram Wed Mar 15 21:16:40 2023 -0700 adding HPRC links to the index pages refs #30508 diff --git src/hg/makeDb/doc/asmHubs/mkAsmStats.pl src/hg/makeDb/doc/asmHubs/mkAsmStats.pl index 03ed644..788338c 100755 --- src/hg/makeDb/doc/asmHubs/mkAsmStats.pl +++ src/hg/makeDb/doc/asmHubs/mkAsmStats.pl @@ -1,436 +1,459 @@ #!/usr/bin/env perl use strict; use warnings; use File::Basename; use FindBin qw($Bin); use lib "$Bin"; use commonHtml; use File::stat; my $argc = scalar(@ARGV); if ($argc != 3) { printf STDERR "mkAsmStats Name asmHubName [two column name list]\n"; printf STDERR "e.g.: mkAsmStats Mammals mammals mammals.asmId.commonName.tsv\n"; printf STDERR "the name list is found in \$HOME/kent/src/hg/makeDb/doc/asmHubs/\n"; printf STDERR "\nthe two columns are 1: asmId (accessionId_assemblyName)\n"; printf STDERR "column 2: common name for species, columns separated by tab\n"; exit 255; } my $home = $ENV{'HOME'}; my $toolsDir = "$home/kent/src/hg/makeDb/doc/asmHubs"; my $Name = shift; my $asmHubName = shift; my $inputList = shift; my $orderList = $inputList; if ( ! -s "$orderList" ) { $orderList = $toolsDir/$inputList; } my @orderList; # asmId of the assemblies in order from the orderList file my %commonName; # key is asmId, value is a common name, perhaps more appropriate # than found in assembly_report file my $vgpIndex = 0; $vgpIndex = 1 if ($Name =~ m/vgp/i); +my $hprcIndex = 0; +$hprcIndex = 1 if ($Name =~ m/hprc/i); my $assemblyTotal = 0; # complete list of assemblies in this group my $asmCount = 0; # count of assemblies completed and in the table my $overallNucleotides = 0; my $overallSeqCount = 0; my $overallGapSize = 0; my $overallGapCount = 0; ############################################################################## # from Perl Cookbook Recipe 2.17, print out large numbers with comma delimiters: ############################################################################## sub commify($) { 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; my $subSetMessage = "subset of $asmHubName only"; if ($asmHubName eq "vertebrate") { $subSetMessage = "subset of other ${asmHubName}s only"; } if ($vgpIndex) { my $vgpSubset = "(set of primary assemblies)"; if ($orderList =~ m/vgp.alternate/) { $vgpSubset = "(set of alternate/haplotype assemblies)"; } elsif ($orderList =~ m/vgp.trio/) { $vgpSubset = "(set of trio assemblies, maternal/paternal)"; } elsif ($orderList =~ m/vgp.legacy/) { $vgpSubset = "(set of legacy/superseded assemblies)"; } print <<"END" <!DOCTYPE HTML 4.01 Transitional> <!--#set var="TITLE" value="VGP - Vertebrate Genomes Project assembly hubs, assembly statistics" --> <!--#set var="ROOT" value="../.." --> <!--#include virtual="\$ROOT/inc/gbPageStartHardcoded.html" --> <h1>VGP - Vertebrate Genomes Project assembly hubs, assembly statistics</h1> <p> <a href='https://vertebrategenomesproject.org/' target=_blank> <img src='VGPlogo.png' width=280 alt='VGP logo'></a></p> <p> This assembly hub contains assemblies released by the <a href='https://vertebrategenomesproject.org/' target=_blank> Vertebrate Genomes Project.</a> $vgpSubset </p> END } else { + if ($hprcIndex) { + print <<"END" +<!DOCTYPE HTML 4.01 Transitional> +<!--#set var="TITLE" value="HPRC - Human Pangenome Reference Consortium assembly hubs, assembly statistics" --> +<!--#set var="ROOT" value="../.." --> + +<!--#include virtual="\$ROOT/inc/gbPageStartHardcoded.html" --> + +<h1>VGP - Human Pangenome Reference Consortium assembly hubs, assembly statistics</h1> +<p> +<a href='https://humanpangenome.org/' target=_blank> +<img src='HPRC_logo.png' width=280 alt='HPRC logo'></a></p> +<p> +This assembly hub contains assemblies released +by the <a href='https://humanpangenome.org/' target=_blank> +Human Pangenome Reference Consortium.</a> +</p> + +END + } else { print <<"END" <!DOCTYPE HTML 4.01 Transitional> <!--#set var="TITLE" value="$Name genomes assembly hubs, assembly statistics" --> <!--#set var="ROOT" value="../.." --> <!--#include virtual="\$ROOT/inc/gbPageStartHardcoded.html" --> <h1>$Name Genomes assembly hubs, assembly statistics</h1> <p> Assemblies from NCBI/Genbank/Refseq sources, $subSetMessage. </p> END } +} print <<"END" <h3>See also: <a href='index.html'>hub access</a>, <a href='trackData.html'>track 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 } ############################################################################## ### 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>sequence<br>count</th><th>genome size<br>nucleotides</th> <th>gap<br>count</th><th>unknown bases<br>(gap size sum)</th><th>masking<br>percent</th> </tr></thead><tbody> END } ############################################################################## ### end the table output ############################################################################## sub endTable() { my $commaNuc = commify($overallNucleotides); my $commaSeqCount = commify($overallSeqCount); my $commaGapSize = commify($overallGapSize); my $commaGapCount = commify($overallGapCount); my $percentDone = 100.0 * $asmCount / $assemblyTotal; my $doneMsg = ""; if ($asmCount < $assemblyTotal) { $doneMsg = sprintf(" (%d build completed, %.2f %% finished)", $asmCount, $percentDone); } if ($assemblyTotal > 1) { print " </tbody> <tfoot><tr><th>TOTALS:</th><td align=center colspan=3>total assembly count ${assemblyTotal}${doneMsg}</td> <td align=right>$commaSeqCount</td> <td align=right>$commaNuc</td> <td align=right>$commaGapCount</td> <td align=right>$commaGapSize</td> <td colspan=1> </td> </tr> "; # try extra column headers as last row for this very large index page if ($vgpIndex && ($asmCount > 15)) { print "<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>sequence<br>count</th><th>genome size<br>nucleotides</th> <th>gap<br>count</th><th>unknown bases<br>(gap size sum)</th><th>masking<br>percent</th> </tr> "; } print " </tfoot> </table> "; } else { print " </tbody> </table> "; } # $assemblyTotal <= 1 } # sub endTable() ############################################################################## ### end the HTML output ############################################################################## sub endHtml() { &commonHtml::otherHubLinks($vgpIndex, $asmHubName); &commonHtml::htmlFooter($vgpIndex, $asmHubName); } sub asmCounts($) { my ($chromSizes) = @_; my ($sequenceCount, $totalSize) = split('\s+', `ave -col=2 $chromSizes | egrep "^count|^total" | awk '{printf "%d\\n", \$NF}' | xargs echo`); return ($sequenceCount, $totalSize); } sub maskStats($) { my ($faSizeFile) = @_; my $gapSize = `grep 'sequences in 1 file' $faSizeFile | awk '{print \$3}'`; chomp $gapSize; $gapSize =~ s/\(//; my $totalBases = `grep 'sequences in 1 file' $faSizeFile | awk '{print \$1}'`; chomp $totalBases; my $maskedBases = `grep 'sequences in 1 file' $faSizeFile | awk '{print \$9}'`; chomp $maskedBases; my $maskPerCent = 100.0 * $maskedBases / $totalBases; return ($gapSize, $maskPerCent); } # grep "sequences in 1 file" GCA_900324465.2_fAnaTes1.2.faSize.txt # 555641398 bases (3606496 N's 552034902 real 433510637 upper 118524265 lower) in 50 sequences in 1 files sub gapStats($$) { my ($buildDir, $asmId) = @_; my $gapBed = "$buildDir/trackData/allGaps/$asmId.allGaps.bed.gz"; my $gapCount = 0; if ($asmId !~ m/^GC/) { $gapBed = "/hive/data/genomes/$asmId/$asmId.N.bed"; if ( -s "$gapBed" ) { $gapCount = `awk '{print \$3-\$2}' $gapBed | ave stdin | grep '^count' | awk '{print \$2}'`; } } elsif ( -s "$gapBed" ) { $gapCount = `zcat $gapBed | awk '{print \$3-\$2}' | ave stdin | grep '^count' | awk '{print \$2}'`; } chomp $gapCount; return ($gapCount); } ############################################################################## ### tableContents() ############################################################################## sub tableContents() { foreach my $asmId (@orderList) { my $gcPrefix = "GCx"; my $asmAcc = "asmAcc"; my $asmName = "asmName"; my $accessionId = "GCx_098765432.1"; my $accessionDir = ""; my $configRa = "n/a"; if ($asmId !~ m/^GC/) { $configRa = "/hive/data/genomes/$asmId/$asmId.config.ra"; $accessionId = `grep ^genBankAccessionID "${configRa}" | cut -d' ' -f2`; chomp $accessionId; $asmName = `grep ^ncbiAssemblyName "${configRa}" | cut -d' ' -f2`; chomp $asmName; $accessionDir = substr($accessionId, 0 ,3); $accessionDir .= "/" . substr($accessionId, 4 ,3); $accessionDir .= "/" . substr($accessionId, 7 ,3); $accessionDir .= "/" . substr($accessionId, 10 ,3); ($gcPrefix, $asmAcc) = split('_', $accessionId, 2); printf STDERR "# %03d\t%s_%s (%s)\n", 1 + $asmCount, $accessionId, $asmName, $asmId; } else { ($gcPrefix, $asmAcc, $asmName) = split('_', $asmId, 3); $accessionId = sprintf("%s_%s", $gcPrefix, $asmAcc); $accessionDir = substr($asmId, 0 ,3); $accessionDir .= "/" . substr($asmId, 4 ,3); $accessionDir .= "/" . substr($asmId, 7 ,3); $accessionDir .= "/" . substr($asmId, 10 ,3); printf STDERR "# %03d\t%s\n", 1 + $asmCount, $asmId; } # assume GCF/refseq build my $buildDir = "/hive/data/genomes/asmHubs/refseqBuild/$accessionDir/$asmId"; if ($gcPrefix eq "GCA") { # this is a GCA/genbank build $buildDir = "/hive/data/genomes/asmHubs/genbankBuild/$accessionDir/$asmId"; } my $asmReport="$buildDir/download/${asmId}_assembly_report.txt"; my $chromSizes = "${buildDir}/${asmId}.chrom.sizes"; my $twoBit = "${buildDir}/trackData/addMask/${asmId}.masked.2bit"; my $faSizeTxt = "${buildDir}/${asmId}.faSize.txt"; if ($asmId !~ m/^GC/) { # this is a UCSC genome database browser $buildDir="/hive/data/outside/ncbi/genomes/$accessionDir/${accessionId}_${asmName}"; $asmReport="$buildDir/${accessionId}_${asmName}_assembly_report.txt"; $chromSizes = "/hive/data/genomes/$asmId/chrom.sizes"; $twoBit = "/hive/data/genomes/$asmId/$asmId.2bit"; $faSizeTxt = "/hive/data/genomes/$asmId/faSize.${asmId}.2bit.txt"; } if (! -s "$asmReport") { printf STDERR "# no assembly report:\n# %s\n", $asmReport; next; } if (! -s "$twoBit") { printf STDERR "# no 2bit file:\n# %s\n", $twoBit; next; } if ( ! -s "$faSizeTxt" ) { printf STDERR "twoBitToFa $twoBit stdout | faSize stdin > $faSizeTxt\n"; print `twoBitToFa $twoBit stdout | faSize stdin > $faSizeTxt`; } my ($gapSize, $maskPerCent) = maskStats($faSizeTxt); $overallGapSize += $gapSize; my ($seqCount, $totalSize) = asmCounts($chromSizes); $overallSeqCount += $seqCount; $overallNucleotides += $totalSize; my $gapCount = gapStats($buildDir, $asmId); $overallGapCount += $gapCount; 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/.*\(//; $commonName =~ s/\)//; $commonName = $commonName{$asmId} if (exists($commonName{$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"; my $browserName = $commonName; my $browserUrl = "https://genome.ucsc.edu/h/$accessionId"; if ($asmId !~ m/^GC/) { $hubUrl = "https://hgdownload.soe.ucsc.edu/goldenPath/$asmId/bigZips"; $browserUrl = "https://genome.ucsc.edu/cgi-bin/hgTracks?db=$asmId"; $browserName = "$commonName ($asmId)"; } printf "<tr><td align=right>%d</td>\n", ++$asmCount; # 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='%s' target=_blank>%s</a></td>\n", $browserUrl, $browserName; printf " <td align=center><a href='%s/' target=_blank>%s</a></td>\n", $hubUrl, $sciName; if ($asmId !~ m/^GC/) { printf " <td align=left><a href='https://www.ncbi.nlm.nih.gov/assembly/%s_%s/' target=_blank>%s_%s</a></td>\n", $gcPrefix, $asmAcc, $accessionId, $asmName; } else { printf " <td align=left><a href='https://www.ncbi.nlm.nih.gov/assembly/%s/' target=_blank>%s</a></td>\n", $accessionId, $asmId; } printf " <td align=right>%s</td>\n", commify($seqCount); printf " <td align=right>%s</td>\n", commify($totalSize); printf " <td align=right>%s</td>\n", commify($gapCount); printf " <td align=right>%s</td>\n", commify($gapSize); printf " <td align=right>%.2f</td>\n", $maskPerCent; printf "</tr>\n"; } } # sub tableContents() ############################################################################## ### main() ############################################################################## # if there is a 'promoted' list, it has been taken out of the 'orderList' # so will need to stuff it back in at the correct ordered location my %promotedList; # key is asmId, value is common name my $promotedList = dirname(${orderList}) . "/promoted.list"; my @promotedList; # contents are asmIds, in order by lc(common name) my $promotedIndex = -1; # to walk through @promotedList; if ( -s "${promotedList}" ) { open (FH, "<${promotedList}" ) or die "can not read ${promotedList}"; while (my $line = <FH>) { next if ($line =~ m/^#/); chomp $line; my ($asmId, $commonName) = split('\t', $line); $promotedList{$asmId} = $commonName; } close (FH); foreach my $asmId ( sort { lc($promotedList{$a}) cmp lc($promotedList{$b}) } keys %promotedList) { push @promotedList, $asmId; } $promotedIndex = 0; } open (FH, "<${orderList}") or die "can not read ${orderList}"; while (my $line = <FH>) { next if ($line =~ m/^#/); chomp $line; my ($asmId, $commonName) = split('\t', $line); if ( ($promotedIndex > -1) && ($promotedIndex < scalar(@promotedList))) { my $checkInsertAsmId = $promotedList[$promotedIndex]; my $checkInsertName = $promotedList{$checkInsertAsmId}; # insert before this commonName when alphabetic before if (lc($checkInsertName) lt lc($commonName)) { push @orderList, $checkInsertAsmId; $commonName{$checkInsertAsmId} = $checkInsertName; ++$assemblyTotal; printf STDERR "# inserting '%s' before '%s' at # %03d\n", $checkInsertName, $commonName, $assemblyTotal; ++$promotedIndex; # only doing one at this time # TBD: will need to improve this for more inserts } } push @orderList, $asmId; $commonName{$asmId} = $commonName; ++$assemblyTotal; } close (FH); startHtml(); startTable(); tableContents(); endTable(); endHtml();