404562a0949bf43b853017fa20a6fc70d22d4ccc
hiram
  Thu Feb 16 11:43:56 2023 -0800
update to GenArk hubs per user requests refs #29545

diff --git src/hg/makeDb/doc/asmHubs/commonNames.pl src/hg/makeDb/doc/asmHubs/commonNames.pl
index 3e7e528..2f60686 100755
--- src/hg/makeDb/doc/asmHubs/commonNames.pl
+++ src/hg/makeDb/doc/asmHubs/commonNames.pl
@@ -44,31 +44,44 @@
   my $extraStrings = "";
   if (length($isolate) && length($cultivar)) {
      $extraStrings = "$cultivar $isolate $yearDate";
   } elsif (length($isolate)) {
      $extraStrings = "$isolate $yearDate";
   } elsif (length($cultivar)) {
      $extraStrings = "$cultivar $yearDate";
   }
   if ( "x${extraStrings}y" eq "xy" ) {
      $extraStrings = "$yearDate";
   }
   my $orgName = `grep -i -m 1 "Organism name:" "${asmRpt}" | tr -d "
"`;
   $orgName =~ s/.*\(//;
   $orgName =~ s/\)//;
   chomp $orgName;
-  if ($orgName eq "viruses") {
+  if ($orgName =~ m/ascomycete|basidiomycete|budding|microsporidian|smut|fungi/) {
+    my ($order, undef) = split('\s', $orgName, 2);
+    $order = "budding yeast" if ($order =~ m/budding/);
+    $order = "smut fungi" if ($order =~ m/smut/);
+    $order = "ascomycetes" if ($order =~ m/ascomycete/);
+    $order = "basidiomycetes" if ($order =~ m/basidiomycete/);
+    my $sciName = `grep -i -m 1 "Organism name:" "${asmRpt}" | tr -d "
"`;
+    chomp $sciName;
+    $sciName =~ s/.*ism name:\s+//i;
+    $sciName =~ s/\s+\(.*\)$//;
+    my @a = split('\s+', $sciName);
+    my $lastN = scalar(@a) - 1;
+    $orgName = "$order " . uc(substr($a[0], 0, 1)) . "." . @a[1..$lastN];
+  } elsif ($orgName eq "viruses") {
     $orgName = `grep -i -m 1 "Organism name:" "${asmRpt}" | tr -d "
"`;
     chomp $orgName;
     $orgName =~ s/.*ism name:\s+//i;
     $orgName =~ s/\s+\(.*\)$//;
   }
   if (length($extraStrings)) {
     printf "%s\t%s (%s)\n", $asmId, $orgName, $extraStrings;
   } else {
     printf "%s\t%s\n", $asmId, $orgName;
   }
 }
 close (FH);
 
 # GCA_003369685.2_UOA_Angus_1_assembly_report.txt
 # Organism name: