9374faeb653ab0653e07e6ba890d6531395ae476
hiram
  Fri May 24 09:59:56 2024 -0700
correctly identify the source for the genes when coming from GCF onto GCA no redmine

diff --git src/hg/utils/automation/asmHubNcbiRefSeq.pl src/hg/utils/automation/asmHubNcbiRefSeq.pl
index e79b908..c254633 100755
--- src/hg/utils/automation/asmHubNcbiRefSeq.pl
+++ src/hg/utils/automation/asmHubNcbiRefSeq.pl
@@ -1,300 +1,311 @@
 #!/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;
 }
 
 my $asmId = shift;
 my @parts = split('_', $asmId, 3);
 my $accession = "$parts[0]_$parts[1]";
 my $namesFile = shift;
 my $trackDataDir = shift;
 my $ncbiRefSeqBbi = "$trackDataDir/ncbiRefSeq/$asmId.ncbiRefSeq.bb";
-my $asmType = "refseq";
+my $srcGff =  `ls $trackDataDir/ncbiRefSeq/download/*_genomic.gff.gz | head -1`;
+chomp $srcGff;
+my $srcAsmId = $asmId;
+my $gcfToGcaLiftedText = "";
+if (length($srcGff) > 10) {
+  $srcAsmId = basename($srcGff);
+  $srcAsmId =~ s/_genomic.gff.gz//;
+  if ($srcAsmId ne $asmId) {
+    $gcfToGcaLiftedText = "RefSeq annotations from $srcAsmId were lifted to this $asmId assembly to provide these gene annotations on this corresponding assembly."
+  }
+}
 my $asmIdPath = &AsmHub::asmIdToPath($asmId);
 my $downloadGtf = "https://hgdownload.soe.ucsc.edu/hubs/$asmIdPath/$accession/genes/$asmId.ncbiRefSeq.gtf.gz";
 
 if ( ! -s $ncbiRefSeqBbi ) {
   printf STDERR "ERROR: can not find $asmId.ncbiRefSeq.bb file\n";
   exit 255;
 }
 
-my @partNames = split('_', $asmId);
+my @partNames = split('_', $srcAsmId);
 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);
 $itemCount = &AsmHub::commify($itemCount);
 $basesCovered = &AsmHub::commify($basesCovered);
 my $totalBasesCmfy = &AsmHub::commify($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>Data Access</h2>
 <p>
 Download <a href='$downloadGtf' target=_blank> $asmId.ncbiRefSeq.gtf.gz </a> GTF file.
 </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> &ndash; all curated and predicted annotations
      provided by RefSeq.</li>
     <li><em>RefSeq Curated</em> &ndash; 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> &ndash; subset of RefSeq All that includes
      those annotations whose accessions begin with XM or XR.</li>
     <li><em>RefSeq Other</em> &ndash; 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> &ndash; 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>${asmId}_genomic.gff.gz</b>
+data files were downloaded from the file <b>${srcAsmId}_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>
 
+$gcfToGcaLiftedText
+
 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>$totalBasesCmfy <b>bases</b><br><br>
 <b>Curated and Predicted Gene count: </b>$itemCount<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);
   $itemCount = &AsmHub::commify($itemCount);
   $basesCovered = &AsmHub::commify($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>
 </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);
   $itemCount = &AsmHub::commify($itemCount);
   $basesCovered = &AsmHub::commify($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>
 </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);
   $itemCount = &AsmHub::commify($itemCount);
   $basesCovered = &AsmHub::commify($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>
 </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_