9578d5ecb6f52b870b436a05ba64844e801b1853
hiram
  Fri Jul 2 15:33:47 2021 -0700
to convert chromAlias table to text version for download directory no redmine

diff --git src/hg/utils/automation/chromAliasToTxt.pl src/hg/utils/automation/chromAliasToTxt.pl
new file mode 100755
index 0000000..f64fac4
--- /dev/null
+++ src/hg/utils/automation/chromAliasToTxt.pl
@@ -0,0 +1,39 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+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";
+}