a71f33ea4a34a46a90957e9b59cd7235cbdff4e9 hiram Mon Aug 3 15:56:12 2026 -0700 adding annotation version notes correctly to ncbiGene.html description page refs #37958 diff --git src/hg/utils/automation/AsmHub.pm src/hg/utils/automation/AsmHub.pm index f2402d09757..f52b71749c3 100755 --- src/hg/utils/automation/AsmHub.pm +++ src/hg/utils/automation/AsmHub.pm @@ -1,179 +1,233 @@ # AsmHub: common routines for building assembly hubs # # DO NOT EDIT the /cluster/bin/scripts copy of this file -- # edit ~/kent/src/hg/utils/automation/AsmHub.pm instead. package AsmHub; use warnings; use strict; use Carp; use File::Basename; use File::stat; use vars qw(@ISA @EXPORT_OK); use Exporter; @ISA = qw(Exporter); # This is a listing of the public methods and variables (which should be # treated as constants) exported by this module: @EXPORT_OK = ( # Support for common command line options: qw( commify asmSize ncbiGeneDescription ), ); # from Perl Cookbook Recipe 2.17, print out large numbers with comma # delimiters, input is a large number with no commas: sub commify($) { my $text = reverse $_[0]; $text =~ s/(\d\d\d)(?=\d)(?!\d*\.)/$1,/g; return scalar reverse $text } # given an asmId.chrom.sizes, return the assembly size from the # sum of column 2: sub asmSize($) { my ($chromSizes) = @_; my $asmSize=`/cluster/bin/x86_64/ave -col=2 $chromSizes | grep "total" | sed -e 's/total //; s/.000000//;'`; chomp $asmSize; return $asmSize; } # given a fully qualified asmId, e.g.: GCA_018504075.1_HG02723.alt.pat.f1_v2 # return the string representating the path: GCA/018/504/075 sub asmIdToPath($) { my ($asmId) = @_; my $gcX = substr($asmId, 0, 3); my $d0 = substr($asmId, 4, 3); my $d1 = substr($asmId, 7, 3); my $d2 = substr($asmId, 10, 3); my $ret = sprintf("%s/%s/%s/%s", $gcX, $d0, $d1, $d2); return $ret; } +# Look up NCBI's own annotation provider/name/date for an accession from +# the 'genark' database's assemblySummary{Genbank,Refseq} table, falling +# back to the ...Historical variant when the accession isn't in the +# current one (a superseded/suppressed assembly). Returns an empty list +# if found in neither. +sub fetchAnnotationInfo($$) { + my ($asmType, $accession) = @_; + my $table = "assemblySummary" . ucfirst($asmType); + foreach my $t ($table, "${table}Historical") { + my $result = `hgsql -N -e 'select annotationProvider,annotationName,annotationDate from $t where assemblyAccession="$accession";' genark 2> /dev/null`; + chomp $result; + next if ($result eq ""); + my ($provider, $name, $date) = split('\t', $result); + $provider = "" if ( ! defined $provider || $provider eq "NULL" ); + $name = "" if ( ! defined $name || $name eq "NULL" ); + $date = "" if ( ! defined $date || $date eq "NULL" ); + return ($provider, $name, $date) if ($provider ne "" || $name ne "" || $date ne ""); + } + return (); +} # fetchAnnotationInfo + # Build the 'ncbiGene' track description HTML body. Used both by # asmHubNcbiGene.pl for the live track, and by doNcbiGene.pl for the # one-track archive hubs it writes under trackData/ncbiGene/archive/ -- # which is why every path is taken explicitly rather than assumed from # the usual trackData/ layout. $archiveNote, if given, is printed as a # lead-in banner ahead of the normal description (used for the archived # copies; the live page passes it undef). sub ncbiGeneDescription($$$$$;$) { my ($bbPath, $statsPath, $chromSizes, $namesFile, $ncbiAsmId, $archiveNote) = @_; if ( ! -s $bbPath ) { printf STDERR "ERROR: can not find %s file\n", $bbPath; exit 255; } my @partNames = split('_', $ncbiAsmId); my $ftpDirPath = sprintf("%s/%s/%s/%s/%s", $partNames[0], substr($partNames[1],0,3), substr($partNames[1],3,3), substr($partNames[1],6,3), $ncbiAsmId); my $asmType = ($partNames[0] =~ m/GCA/) ? "genbank" : "refseq"; + # bare accession (GCF_937001465.1), not the full asmId with its + # _assemblyName suffix -- used both for the genark annotation lookup + # below and for the archived-hub links further down. + my $accession = "$partNames[0]_$partNames[1]"; + # the .bb's mtime is stamped from the source gff's own mtime (see the # 'touch -r $gffFile' step in doNcbiGene.pl), so it doubles as this # track's own version/build date -- the same convention archiving uses # to name archive// directories, which is why this lines up with # the dates listed under "Archived versions" below. my ($mday,$mon,$year) = (localtime(stat($bbPath)->mtime))[3,4,5]; my $dataVersion = sprintf("%04d-%02d-%02d", $year+1900, $mon+1, $mday); my $totalBases = asmSize($chromSizes); my $geneStats = `cat $statsPath | awk '{printf "%d\\n", \$2}' | xargs echo`; chomp $geneStats; my ($itemCount, $basesCovered) = split('\s+', $geneStats); my $percentCoverage = sprintf("%.3f", 100.0 * $basesCovered / $totalBases); $itemCount = commify($itemCount); $basesCovered = commify($basesCovered); my $totalBasesText = commify($totalBases); my $em = ""; my $noEm = ""; my $assemblyDate = `grep -v "^#" $namesFile | cut -f9`; chomp $assemblyDate; my $organism = `grep -v "^#" $namesFile | cut -f5`; chomp $organism; my $html = ""; $html .= "

$archiveNote

\n\n" if ($archiveNote); if ( "${asmType}" eq "refseq" ) { $html .= <<_EOF_;

Description

The NCBI Gene track for the $assemblyDate $em${organism}$noEm/$ncbiAsmId genome assembly is constructed from the gff file ${ncbiAsmId}_genomic.gff.gz supplied with the genome assembly at the FTP location:
https://ftp.ncbi.nlm.nih.gov/genomes/all/$ftpDirPath/

_EOF_ } else { $html .= <<_EOF_;

Description

The Gene model track for the $assemblyDate $em${organism}$noEm/$ncbiAsmId genome assembly is constructed from the gff file ${ncbiAsmId}_genomic.gff.gz supplied with the genome assembly at the FTP location:
https://ftp.ncbi.nlm.nih.gov/genomes/all/$ftpDirPath/

The gene models were constructed by the submitter of the assembly to the NCBI assembly release system.

_EOF_ } $html .= <<_EOF_;

Track statistics summary

Data version: $dataVersion
Total genome size: $totalBasesText
Gene count: $itemCount
Bases in genes: $basesCovered
Percent genome coverage: % $percentCoverage

_EOF_ + # Only the live page gets NCBI's own annotation source info -- the + # genark tables hold NCBI's current-as-of-now metadata for this + # accession, not a per-archived-snapshot history, so showing it under + # an "archived version" banner would misleadingly imply it describes + # that old snapshot specifically. + if ( ! $archiveNote ) { + my ($annotationProvider, $annotationName, $annotationDate) = + fetchAnnotationInfo($asmType, $accession); + if ($annotationProvider ne "" || $annotationName ne "" || $annotationDate ne "") { + my $showProvider = $annotationProvider; + my $showName = $annotationName; + if ($showName ne "") { + (my $stripped = $showName) =~ s/^Annotation submitted by\s*//i; + $stripped =~ s/^\s+|\s+$//g; + my $providerTrim = $showProvider; + $providerTrim =~ s/^\s+|\s+$//g; + # if the name is just "Annotation submitted by ", the + # name adds nothing over the provider field -- show it only when + # the two are actually different + $showName = ($providerTrim ne "" && lc($stripped) eq lc($providerTrim)) + ? "" : $stripped; + } + $html .= "

Annotation source

\n

\n"; + $html .= "Annotation provider: $showProvider
\n" if ($showProvider ne ""); + $html .= "Annotation name: $showName
\n" if ($showName ne ""); + $html .= "Annotation date: $annotationDate
\n" if ($annotationDate ne ""); + $html .= "

\n\n"; + } + } + # Only the live page advertises archives (an archived page's own # description already carries $archiveNote and has nothing further # under it to list). Archived copies are published to hgdownload at # https://hgdownload.soe.ucsc.edu/hubs///archive/ncbiGene//hub.txt # -- one self-contained hub.txt per version -- regardless of where they # sit in the local build tree, so we just need the version list. if ( ! $archiveNote ) { my $archiveBase = dirname($bbPath) . "/archive"; my @versions = (); if ( -d $archiveBase ) { opendir(my $dh, $archiveBase); if ($dh) { @versions = sort { $b cmp $a } grep { -d "$archiveBase/$_" && $_ !~ m/^\./ } readdir($dh); closedir($dh); } } if (@versions) { - my @parts = split('_', $ncbiAsmId); - my $accession = "$parts[0]_$parts[1]"; my $hashedPath = asmIdToPath($ncbiAsmId); $html .= "

Archived versions

\n

\n"; $html .= "Earlier versions of this track, from before NCBI updated the source annotation, remain available as standalone track hubs:\n"; $html .= "

\n
    \n"; foreach my $version (@versions) { my $hubUrl = "https://hgdownload.soe.ucsc.edu/hubs/$hashedPath/$accession/archive/ncbiGene/$version/hub.txt"; my $url = "/cgi-bin/hgTracks?genome=$accession&hubUrl=$hubUrl"; $html .= "
  • $version
    • \n"; } $html .= "
\n\n"; } } return $html; } # ncbiGeneDescription 1;