428bacd2dcbaca9304763d3f2dca7ccffd088caa hiram Tue May 26 11:18:06 2020 -0700 correct br tags refs #23734 diff --git src/hg/utils/automation/asmHubNcbiRefSeq.pl src/hg/utils/automation/asmHubNcbiRefSeq.pl index 48c4d58..60097d0 100755 --- src/hg/utils/automation/asmHubNcbiRefSeq.pl +++ src/hg/utils/automation/asmHubNcbiRefSeq.pl @@ -1,299 +1,299 @@ #!/usr/bin/env perl use strict; use warnings; use FindBin qw($Bin); use lib "$Bin"; use AsmHub; use File::Basename; my $argc = scalar(@ARGV); if ($argc != 3) { printf STDERR "usage: asmHubNcbiGene.pl asmId asmId.names.tab .../trackData/\n"; printf STDERR "where asmId is the assembly identifier,\n"; printf STDERR "and .../trackData/ is the path to the /trackData/ directory.\n"; exit 255; } # 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 } my $asmId = shift; my $namesFile = shift; my $trackDataDir = shift; my $ncbiRefSeqBbi = "$trackDataDir/ncbiRefSeq/$asmId.ncbiRefSeq.bb"; my $asmType = "refseq"; if ( ! -s $ncbiRefSeqBbi ) { printf STDERR "ERROR: can not find $asmId.ncbiRefSeq.bb file\n"; exit 255; } my @partNames = split('_', $asmId); 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), $asmId); $asmType = "genbank" if ($partNames[0] =~ m/GCA/); my $totalBases = `ave -col=2 $trackDataDir/../${asmId}.chrom.sizes | grep "^total" | awk '{printf "%d", \$2}'`; chomp $totalBases; my $geneStats = `cat $trackDataDir/ncbiRefSeq/${asmId}.ncbiRefSeq.stats.txt | 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 $totalBasesCmfy = commify($totalBases); my $em = "<em>"; my $noEm = "</em>"; my $assemblyDate = `grep -v "^#" $namesFile | cut -f9`; chomp $assemblyDate; my $ncbiAssemblyId = `grep -v "^#" $namesFile | cut -f10`; chomp $ncbiAssemblyId; my $organism = `grep -v "^#" $namesFile | cut -f5`; chomp $organism; print <<_EOF_ <h2>Description</h2> <p> The NCBI RefSeq Genes composite track shows $assemblyDate $em${organism}$noEm/$asmId protein-coding and non-protein-coding genes taken from the NCBI RNA reference sequences collection (RefSeq). All subtracks use coordinates provided by RefSeq. See the <a href="#methods">Methods</a> section for more details about how the different tracks were created. </p> <p> Please visit NCBI's <a href="https://www.ncbi.nlm.nih.gov/projects/RefSeq/update.cgi" target="_blank"> Feedback for Gene and Reference Sequences (RefSeq)</a> page to make suggestions, submit additions and corrections, or ask for help concerning RefSeq records. </p> <p> For more information on the different gene tracks, see our <a target=_blank href="/FAQ/FAQgenes.html">Genes FAQ</a>. </p> <h2>Display Conventions and Configuration</h2> <p> To show only a selected set of subtracks, uncheck the boxes next to the tracks that you wish to hide. </p> The tracks available here can include (not all may be present): <dl> <dt><em><strong>RefSeq annotations and alignments</strong></em></dt> <ul> <li><em>RefSeq All</em> – all curated and predicted annotations provided by RefSeq.</li> <li><em>RefSeq Curated</em> – subset of <em>RefSeq All</em> that includes only those annotations whose accessions begin with NM, NR, NP or YP. <small>(NP and YP are used only for protein-coding genes on the mitochondrion; YP is used for human only.)</small></li> <li><em>RefSeq Predicted</em> – subset of RefSeq All that includes those annotations whose accessions begin with XM or XR.</li> <li><em>RefSeq Other</em> – all other annotations produced by the RefSeq group that do not fit the requirements for inclusion in the <em>RefSeq Curated</em> or the <em>RefSeq Predicted</em> tracks.</li> <li> <em>RefSeq Alignments</em> – alignments of RefSeq RNAs to the $assemblyDate $em${organism}$noEm/$asmId genome provided by the RefSeq group.</li> </ul> </dl> <p> The <em>RefSeq All</em>, <em>RefSeq Curated</em> and <em>RefSeq Predicted</em>, tracks follow the display conventions for <a href="../goldenPath/help/hgTracksHelp.html#GeneDisplay" target="_blank">gene prediction tracks</a>. The color shading indicates the level of review the RefSeq record has undergone: predicted (light), provisional (medium), or reviewed (dark), as defined by <a target=_blank href="https://www.ncbi.nlm.nih.gov/books/NBK21091/table/ch18.T.refseq_status_codes/?report=objectonly">RefSeq</a>. </p> <p> <table> <thead> <tr> <th style="border-bottom: 2px solid #6678B1;">Color</th> <th style="border-bottom: 2px solid #6678B1;">Level of review</th> </tr> </thead> <tr> <th bgcolor="#0C0C78"></th> <th align="left">Reviewed: the RefSeq record has been reviewed by NCBI staff or by a collaborator. The NCBI review process includes assessing available sequence data and the literature. Some RefSeq records may incorporate expanded sequence and annotation information.</th> </tr> <tr> <th bgcolor="#5050A0"></th> <th align="left">Provisional: the RefSeq record has not yet been subject to individual review. The initial sequence-to-gene association has been established by outside collaborators or NCBI staff.</th> </tr> <tr> <th bgcolor="#8282D2"></th> <th align="left">Predicted: the RefSeq record has not yet been subject to individual review, and some aspect of the RefSeq record is predicted.</th> </tr> </table> </p> The <em>RefSeq Alignments</em> track follows the display conventions for <a href="../goldenPath/help/hgTracksHelp.html#PSLDisplay" target="_blank">PSL tracks</a>.</p> <p> The item labels and codon display properties for features within this track can be configured through the controls at the top of the track description page. To adjust the settings for an individual subtrack, click the wrench icon next to the track name in the subtrack list. </p> <ul> <li><strong>Label:</strong> By default, items are labeled by gene name. Click the appropriate Label option to display the accession name or OMIM identifier instead of the gene name, show all or a subset of these labels including the gene name, OMIM identifier and accession names, or turn off the label completely.</li> <li><strong>Codon coloring:</strong> This track has an optional codon coloring feature that allows users to quickly validate and compare gene predictions. To display codon colors, select the <em>genomic codons</em> option from the <em>Color track by codons</em> pull-down menu. For more information about this feature, go to the <a href="../goldenPath/help/hgCodonColoring.html" target="_blank">Coloring Gene Predictions and Annotations by Codon</a> page.</li> </ul> <a name="methods"></a> <h2>Methods</h2> <p> The RefSeq annotation and RefSeq RNA alignment tracks were created at UCSC using data from the NCBI RefSeq project. GFF format data files were downloaded from the file <b>${asmId}_genomic.gff.gz</b> delivered with the NCBI RefSeq genome assemblies at the FTP location:<br> <a href='ftp://ftp.ncbi.nlm.nih.gov/genomes/all/$ftpDirPath/' target='_blank'>ftp://ftp.ncbi.nlm.nih.gov/genomes/all/$ftpDirPath/</a> The GFF file was converted to the genePred and PSL table formats for display in the Genome Browser. Information about the NCBI annotation pipeline can be found <a href="https://www.ncbi.nlm.nih.gov/genome/annotation_euk/process/" target="_blank">here</a>. </p> <h2>Track statistics summary</h2> <p> -<b>Total genome size: </b>$totalBasesCmfy <b>bases<b></br><br> +<b>Total genome size: </b>$totalBasesCmfy <b>bases</b><br><br> <b>Curated and Predicted Gene count: </b>$itemCount<br> -<b>Bases in these genes: </b>$basesCovered</br> -<b>Percent genome coverage: </b>% $percentCoverage</br> +<b>Bases in these genes: </b>$basesCovered<br> +<b>Percent genome coverage: </b>% $percentCoverage<br> </p> _EOF_ ; if ( -s "$trackDataDir/ncbiRefSeq/${asmId}.ncbiRefSeqCurated.stats.txt" ) { $geneStats = `cat $trackDataDir/ncbiRefSeq/${asmId}.ncbiRefSeqCurated.stats.txt | awk '{printf "%d\\n", \$2}' | xargs echo`; chomp $geneStats; ($itemCount, $basesCovered) = split('\s+', $geneStats); $percentCoverage = sprintf("%.3f", 100.0 * $basesCovered / $totalBases); $itemCount = commify($itemCount); $basesCovered = commify($basesCovered); printf <<_EOF_ <p> <b>Curated gene count: </b>$itemCount<br> -<b>Bases in curated genes: </b>$basesCovered</br> -<b>Percent genome coverage: </b>% $percentCoverage</br> +<b>Bases in curated genes: </b>$basesCovered<br> +<b>Percent genome coverage: </b>% $percentCoverage<br> </p> _EOF_ } else { printf <<_EOF_ <p> <b>There are no curated gene annotations.</b> </p> _EOF_ } if ( -s "$trackDataDir/ncbiRefSeq/${asmId}.ncbiRefSeqPredicted.stats.txt" ) { $geneStats = `cat $trackDataDir/ncbiRefSeq/${asmId}.ncbiRefSeqPredicted.stats.txt | awk '{printf "%d\\n", \$2}' | xargs echo`; chomp $geneStats; ($itemCount, $basesCovered) = split('\s+', $geneStats); $percentCoverage = sprintf("%.3f", 100.0 * $basesCovered / $totalBases); $itemCount = commify($itemCount); $basesCovered = commify($basesCovered); printf <<_EOF_ <p> <b>Predicted gene count: </b>$itemCount<br> -<b>Bases in genes: </b>$basesCovered</br> -<b>Percent genome coverage: </b>% $percentCoverage</br> +<b>Bases in genes: </b>$basesCovered<br> +<b>Percent genome coverage: </b>% $percentCoverage<br> </p> _EOF_ } else { printf <<_EOF_ <p> <b>there are no predicted gene annotations</b> </p> _EOF_ } if ( -s "$trackDataDir/ncbiRefSeq/${asmId}.ncbiRefSeqOther.stats.txt" ) { $geneStats = `cat $trackDataDir/ncbiRefSeq/${asmId}.ncbiRefSeqOther.stats.txt | awk '{printf "%d\\n", \$2}' | xargs echo`; chomp $geneStats; ($itemCount, $basesCovered) = split('\s+', $geneStats); $percentCoverage = sprintf("%.3f", 100.0 * $basesCovered / $totalBases); $itemCount = commify($itemCount); $basesCovered = commify($basesCovered); printf <<_EOF_ <p> <b>Other annotation count: </b>$itemCount<br> -<b>Bases in other annotations: </b>$basesCovered</br> -<b>Percent genome coverage: </b>% $percentCoverage</br> +<b>Bases in other annotations: </b>$basesCovered<br> +<b>Percent genome coverage: </b>% $percentCoverage<br> </p> _EOF_ } printf <<_EOF_ <h2>Credits</h2> <p> This track was produced at UCSC from data generated by scientists worldwide and curated by the NCBI RefSeq project. </p> <h2>References</h2> <p> Kent WJ. <a href="https://genome.cshlp.org/content/12/4/656.full" target="_blank">BLAT - the BLAST-like alignment tool</a>. <em>Genome Res.</em> 2002 Apr;12(4):656-64. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/11932250" target="_blank">11932250</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC187518/" target="_blank">PMC187518</a> </p> <p> Pruitt KD, Brown GR, Hiatt SM, Thibaud-Nissen F, Astashyn A, Ermolaeva O, Farrell CM, Hart J, Landrum MJ, McGarvey KM <em>et al</em>. <a href="https://academic.oup.com/nar/article/42/D1/D756/1051112/RefSeq-an-update-on-mammalian-reference-sequences" target="_blank">RefSeq: an update on mammalian reference sequences</a>. <em>Nucleic Acids Res</em>. 2014 Jan;42(Database issue):D756-63. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/24259432" target="_blank">24259432</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965018/" target="_blank">PMC3965018</a> </p> <p> Pruitt KD, Tatusova T, Maglott DR. <a href="https://academic.oup.com/nar/article/33/suppl_1/D501/2505241/NCBI-Reference-Sequence-RefSeq-a-curated-non" target="_blank"> NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins</a>. <em>Nucleic Acids Res.</em> 2005 Jan 1;33(Database issue):D501-4. PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/15608248" target="_blank">15608248</a>; PMC: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC539979/" target="_blank">PMC539979</a> </p> _EOF_