1a2aa31bfa14f809ee4093cea7b436e331b86ff4
hiram
  Thu Feb 16 14:56:34 2023 -0800
improved common names for fungi and bacteria an lower limits for valid number of tracks in bacteria and plants refs #29545

diff --git src/hg/makeDb/doc/asmHubs/commonNames.pl src/hg/makeDb/doc/asmHubs/commonNames.pl
index 2f60686..f0a052a 100755
--- src/hg/makeDb/doc/asmHubs/commonNames.pl
+++ src/hg/makeDb/doc/asmHubs/commonNames.pl
@@ -14,78 +14,90 @@
 my $ncbiSrc="/hive/data/outside/ncbi/genomes";
 
 my $listFile = shift;
 open (FH, "<$listFile") or die "can not open $listFile";
 while (my $asmId = <FH>) {
   next if ($asmId =~ m/^#/);
   $asmId =~ s/\s+.*//;
   chomp $asmId;
   next if (length($asmId) < 1);
   my $gcx = substr($asmId, 0, 3);
   my $id0 = substr($asmId, 4, 3);
   my $id1 = substr($asmId, 7, 3);
   my $id2 = substr($asmId, 10, 3);
   my $srcDir = sprintf "%s/%s/%s/%s/%s/%s", $ncbiSrc, $gcx, $id0, $id1, $id2, $asmId;
   my $asmRpt = "$srcDir/${asmId}_assembly_report.txt";
+  my $sciName = `grep -i -m 1 "Organism name:" "${asmRpt}" | tr -d "
"`;
+  chomp $sciName;
+  $sciName =~ s/.*ism name:\s+//i;
+  $sciName =~ s/\s+\(.*\)$//;
   my $yearDate = `grep -i -m 1 "Date:" "${asmRpt}" | tr -d "
" | awk '{print \$NF}' | sed -e 's/-.*//;'`;
   chomp $yearDate;
   my $isolate = `grep -i -m 1 "Isolate:" "${asmRpt}" | tr -d "
"`;
   chomp $isolate;
   if (length($isolate)) {
     $isolate =~ s/.*solate: *//;
   }
   my $cultivar = `grep -i -m 1 "Infraspecific name:" "${asmRpt}" | tr -d "
"`;
   chomp $cultivar;
   if (length($cultivar)) {
     $cultivar =~ s/.*cultivar=//;
     $cultivar =~ s/.*ecotype=//;
     $cultivar =~ s/.*strain=//;
     $cultivar =~ s/.*breed=//;
   }
   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 =~ m/ascomycete|basidiomycete|budding|microsporidian|smut|fungi/) {
+  if ($orgName =~ m/firmicutes|proteobacteria|high G|enterobacteria|agent of/) {
+#    my @a = split('\s+', $sciName);
+#    my $lastN = scalar(@a) - 1;
+#    $orgName = uc(substr($a[0], 0, 1)) . "." . @a[1..$lastN];
+    $orgName = $sciName;
+  } elsif ($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)) {
+    my @a = split('\s+', $extraStrings);
+    for (my $i = 0; $i < scalar(@a); ++$i) {
+        $orgName =~ s/$a[$i]//;
+    }
+    $orgName =~ s/=//g;
+    $orgName =~ s/  / /g;
+    $orgName =~ s/ +$//;
     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:
 
 # GCF_010993605.1_kPetMar1.pri
 # GCF_900246225.1_fAstCal1.2