60cbd8384a71282078c4651971c1c8857aa3be23
hiram
  Thu Nov 10 11:25:22 2022 -0800
not necessary to include both Case and non case strings ix is all lower case no redmine

diff --git src/hg/utils/automation/xenoRefGeneIx.pl src/hg/utils/automation/xenoRefGeneIx.pl
index cdd67ee..1e7ea49 100755
--- src/hg/utils/automation/xenoRefGeneIx.pl
+++ src/hg/utils/automation/xenoRefGeneIx.pl
@@ -41,60 +41,51 @@
 
 if ($argc != 1 ) {
   printf STDERR "usage: xenoRefGeneIx.pl <bpgInput.txt> | sort -u > ix.txt\n";
   printf STDERR "then run ixIxx on ix.txt:\n";
   printf STDERR " ixIxx ix.txt out.ix out.ixx\n";
   exit 255;
 }
 
 # some of the Arabidopsis thaliana genes are coming in as pairs
 # of different names separated by '; ', process both names
 
 sub processOne($$) {
   my ($nameHash, $someName) = @_;
   if ($someName =~ m/; /) {
     my ($name1, $name2) = split('; ', $someName);
-    $nameHash->{$name1} += 1;
-    $nameHash->{$name2} += 1;
     $nameHash->{lc($name1)} += 1;
     $nameHash->{lc($name2)} += 1;
     my $noSuffix = $name1;
     $noSuffix =~ s/\.[0-9][0-9]*$//;
-    $nameHash->{$noSuffix} += 1;
     $nameHash->{lc($noSuffix)} += 1;
     $noSuffix = $name2;
     $noSuffix =~ s/\.[0-9][0-9]*$//;
-    $nameHash->{$noSuffix} += 1;
     $nameHash->{lc($noSuffix)} += 1;
   } elsif ($someName =~ m/\s/) {
-    $nameHash->{$someName} += 1;
     $nameHash->{lc($someName)} += 1;
     my @names = split('\s+', $someName);
     foreach my $name (@names) {
-      $nameHash->{$name} += 1;
       $nameHash->{lc($name)} += 1;
       my $noSuffix = $name;
       $noSuffix =~ s/\.[0-9][0-9]*$//;
-      $nameHash->{$noSuffix} += 1;
       $nameHash->{lc($noSuffix)} += 1;
     }
   } else {
-    $nameHash->{$someName} += 1;
     $nameHash->{lc($someName)} += 1;
     my $noSuffix = $someName;
     $noSuffix =~ s/\.[0-9][0-9]*$//;
-    $nameHash->{$noSuffix} += 1;
     $nameHash->{lc($noSuffix)} += 1;
   }
 }
 
 my $gpFile = shift;
 
 if ($gpFile =~ m/.gz$/) {
   open (FH, "zcat $gpFile|") or die "ERROR: xenoRefGeneIx.pl can not read '$gpFile'";
 } else {
   open (FH, "<$gpFile") or die "ERROR: xenoRefGeneIx.pl can not read '$gpFile'";
 }
 while (my $line = <FH>) {
   next if ($line =~ m/^#/);
   chomp ($line);
   my ($chrom, $chromStart, $chromEnd, $name, $score, $strand, $thickStart, $thickEnd, $reserved, $blockCount, $blockSizes, $chromStarts, $name2, $cdsStartStat, $cdsEndStat, $exonFrames, $type, $geneName, $geneName2, $geneType) = split('\t', $line);