b7d1b1b10c2fa9a037b3104bb2540e02da60e3ec
hiram
  Mon Feb 13 10:39:47 2023 -0800
replace the obsolete chromAliasToTxt.pl with the aliasTabToText.pl equivalent no redmine

diff --git src/hg/utils/automation/chromAliasToTxt.pl src/hg/utils/automation/chromAliasToTxt.pl
index f64fac4..188b249 100755
--- src/hg/utils/automation/chromAliasToTxt.pl
+++ src/hg/utils/automation/chromAliasToTxt.pl
@@ -1,39 +1,44 @@
 #!/usr/bin/env perl
 
 use strict;
 use warnings;
 
+printf STDERR "# # # ! ! ! Obsolete program, please instead use:\n";
+printf STDERR "  aliasTabToText.pl asmId.chromAlias.tab > asmId.chromAlias.txt\n";
+
+exit 255;
+__END__
 my $argc = scalar(@ARGV);
 
 if ($argc !=1 ) {
   printf STDERR "usage: chromAliasToTxt.pl ucscDb > ucscDb.chromAlias.txt\n";
   printf STDERR "expecting to find chromAlias table in ucscDb\n";
   exit 255;
 }
 
 my %chrAliases;	# key is chrom name, value is hash pointer to
                 # key is alias name, value is count of times seen
 
 my $ucscDb = shift;
 open (FH, "hgsql -N -e 'select * from chromAlias;' $ucscDb|") or die "can not select from $ucscDb.chromAlias";
 while (my $line = <FH>) {
   chomp $line;
   my ($alias, $chrom, $source) = split('\s+', $line);
   if (! defined($chrAliases{$chrom})) {
      my %h;
      $chrAliases{$chrom} = \%h;
   }
   my $aliases = $chrAliases{$chrom};
   $aliases->{$alias} += 1;
 }
 close (FH);
 
 printf "# sequenceName\talias names\tUCSC database: $ucscDb\n";
 foreach my $chr (sort keys %chrAliases) {
   my $aliases = $chrAliases{$chr};
   printf "%s", $chr;
   foreach my $alias (sort keys %$aliases) {
     printf "\t%s", $alias;
   }
   printf "\n";
 }