9bfef693a8110e2a27a49ecd834ff3f875aecb76
hiram
  Fri Jan 8 14:36:20 2021 -0800
better decision on when to be refseq asmHub refs #24396

diff --git src/hg/utils/automation/asmHubGatewayPage.pl src/hg/utils/automation/asmHubGatewayPage.pl
index 5024ee8..07b361e 100755
--- src/hg/utils/automation/asmHubGatewayPage.pl
+++ src/hg/utils/automation/asmHubGatewayPage.pl
@@ -167,31 +167,31 @@
 $accessionDir .= "/" . substr($asmId, 7 ,3);
 $accessionDir .= "/" . substr($asmId, 10 ,3);
 $accessionDir .= "/" . $accessionId;
 
 my $newStyleUrl = sprintf("%s/%s/%s/%s/%s", $gcXPrefix, substr($accession,0,3),
    substr($accession,3,3), substr($accession,6,3), $asmId);
 my $localDataUrl = sprintf("%s/%s/%s/%s/%s", $gcXPrefix, substr($accession,0,3),
    substr($accession,3,3), substr($accession,6,3), $accessionId);
 $ftpName =~ s#/hive/data/outside/ncbi/##;
 $ftpName =~ s#/hive/data/inside/ncbi/##;
 $ftpName =~ s#/hive/data/genomes/asmHubs/##;
 # my $urlDirectory = `basename $ftpName`;
 # chomp $urlDirectory;
 my $speciesSubgroup = $ftpName;
 my $asmType = "genbank";
-$asmType = "refseq" if ( $speciesSubgroup =~ m#refseq/#);
+$asmType = "refseq" if ( $gcXPrefix =~ m#GCF#);
 $speciesSubgroup =~ s#genomes/$asmType/##;;
 $speciesSubgroup =~ s#/.*##;;
 
 my %taxIdCommonName;  # key is taxId, value is common name
                       # from NCBI taxonomy database dump
 open (FH, "<$ENV{'HOME'}/kent/src/hg/utils/automation/genbank/taxId.comName.tab") or die "can not read taxId.comName.tab";
 while (my $line = <FH>) {
   chomp $line;
   my ($taxId, $comName) = split('\t', $line);
   $taxIdCommonName{$taxId} = $comName;
 }
 close (FH);
 
 
 my $submitter = "(n/a)";