037a404d5b76d3005d0263ef6212066e3073ea4a
galt
  Fri Apr 23 02:27:58 2021 -0700
altScaffoldPlacementToBed.pl handle MMCHR scaffold fix on alt for mouse.

diff --git src/hg/utils/automation/altScaffoldPlacementToBed.pl src/hg/utils/automation/altScaffoldPlacementToBed.pl
index 136809f..b56c0a9 100755
--- src/hg/utils/automation/altScaffoldPlacementToBed.pl
+++ src/hg/utils/automation/altScaffoldPlacementToBed.pl
@@ -1,73 +1,78 @@
 #!/usr/bin/env perl
 
 # Convert NCBI assembly alt_scaffold_placement.txt to BED4 that relates alt and fix sequences
 # to chromosome locations (or in one case as of 6/20/18, alt to fix).
 # Optionally use *_assembly_report.txt file to determine alt vs. fix status -- default to guessing
 # based on whether the Assembly name ends in "_PATCH".  (That doesn't work for alt HG1133_PATCH!)
 
 use Getopt::Long;
 use warnings;
 use strict;
 
 use vars qw/$opt_db $opt_assemblyReport/;
 
 my $ok = GetOptions('db=s',
                     'assemblyReport=s');
 
 my %aNameToSuffix = ();
 if ($opt_assemblyReport) {
   open(my $F, $opt_assemblyReport) || die "Can't open $opt_assemblyReport: $!\n";
   while (<$F>) {
     next if (/^#/);
     my ($name, $type) = split("\t");
     my $suffix;
     if ($type eq 'alt-scaffold' || $type eq 'novel-patch') {
       $suffix = 'alt';
     } elsif ($type eq 'fix-patch') {
       $suffix = 'fix';
     }
     if ($suffix) {
       $aNameToSuffix{$name} = $suffix;
     }
   }
   close($F);
 }
 
 while (<>) {
   next if (/^#/);
   chomp;
   my @w = split("\t");
   my ($altScafName, $altAcc, $c, $cAcc, $altStart, $altEnd, $cStart, $cEnd, $altEndTail) =
        ($w[2], $w[3], $w[5], $w[6], $w[9], $w[10], $w[11], $w[12], $w[14]);
   my $suffix = $aNameToSuffix{$altScafName};
   if (! $suffix) {
     $suffix = ($altScafName =~ m/PATCH$/) ? "fix" : "alt";
   }
   my $chr = "chr$c";
   my $chrBase = $chr;
-  if ($c =~ m/^HSCHR/) {
+  if ($c =~ m/^HSCHR/ || $c =~ m/^MMCHR/) {
     # Mapping is not alt/fix to chrom, but fix to alt; convert alt accession to UCSC format:
     $chr = $cAcc;
     if ($opt_db && ($opt_db eq 'hg19' || $opt_db eq 'mm10')) {
       $chr =~ s/^(\w+)\.\d+/$1/ || die "Unexpected cAcc ($cAcc)";
       $chr = lc($chr);
     } else {
       $chr =~ s/^(\w+)\.(\d+)/$1v$2/ || die "Unexpected cAcc ($cAcc)";
     }
+    if ($c =~ m/^HSCHR/) {
       $chrBase =~ s/HSCHR([A-Z0-9]+)_.*/$1/;
+    }
+    if ($c =~ m/^MMCHR/) {
+      $chrBase =~ s/MMCHR([A-Z0-9]+)_.*/$1/;
+    }
     $chr = "${chrBase}_${chr}_alt";
   }
   if ($opt_db && ($opt_db eq 'hg19' || $opt_db eq 'mm10')) {
     $altAcc =~ s/^(\w+)\.\d+/$1/ || die "Unexpected altAcc ($altAcc)";
     $altAcc = lc($altAcc);
   } else {
     $altAcc =~ s/^(\w+)\.(\d+)/$1v$2/ || die "Unexpected altAcc ($altAcc)";
   }
   $altAcc = "${chrBase}_${altAcc}_$suffix";
   my $altName = $altAcc;
   if ($altStart > 1 || $altEndTail > 0) {
     $altName .= ":$altStart-$altEnd";
   }
   print join("\t", $chr, $cStart-1, $cEnd, $altName) . "\n";
   print join("\t", $altAcc, $altStart-1, $altEnd, $chr.":$cStart-$cEnd") . "\n";
 }