adbcbc19d8a90533fc04a2c6a164786fd10e945b hiram Sat Sep 24 18:42:41 2022 -0700 and yet one final name change for T2T-CHM13 refs @29982 diff --git src/hg/utils/automation/HgAutomate.pm src/hg/utils/automation/HgAutomate.pm index c8c6b8a..7534b16 100755 --- src/hg/utils/automation/HgAutomate.pm +++ src/hg/utils/automation/HgAutomate.pm @@ -744,31 +744,31 @@ if ($accession !~ m/^GC/) { # not a GenArk hub, database assembly my ($comName, $asmDate, $submitter) = getAssemblyInfo("hgwdev", $accession); $returnDate = $asmDate; $returnAsmName = $accession; } else { my $gcX = substr($accession, 0, 3); my $d0 = substr($accession, 4, 3); my $d1 = substr($accession, 7, 3); my $d2 = substr($accession, 10, 3); # a couple assemblies unfortunately have two different assembly names # can't work with those with just an accession # special case the CHM13 assembly my $betterId = $accession; if ($accession =~ m/GCA_009914755.4/) { - $betterId = "GCA_009914755.4_CHM13_T2T_v2.0"; + $betterId = "GCA_009914755.4_T2T-CHM13v2.0"; } my $dirCount = `ls -d /hive/data/outside/ncbi/genomes/$gcX/$d0/$d1/$d2/${betterId}* | wc -l`; chomp $dirCount; if (1 == $dirCount) { my $srcDir = `ls -d /hive/data/outside/ncbi/genomes/$gcX/$d0/$d1/$d2/${betterId}*`; chomp $srcDir; if ( -d "${srcDir}" ) { my $asmId = basename($srcDir); my $asmRpt = "$srcDir/${asmId}_assembly_report.txt"; if ( -s "${asmRpt}" ) { (undef, undef, $returnAsmName) = split('_', $asmId, 3); if (defined($returnAsmName)) { $returnAsmName =~ s/\r//; $returnAsmName =~ s/^/_/; } else {