123fabea3a7c3d2877818bfe27bcfaf49bbf0c58
hiram
  Mon Dec 14 22:52:47 2020 -0800
beware blanks in sequence names refs #23891

diff --git src/hg/utils/automation/asmHubChromAlias.pl src/hg/utils/automation/asmHubChromAlias.pl
index db4c464..d43d5aa 100755
--- src/hg/utils/automation/asmHubChromAlias.pl
+++ src/hg/utils/automation/asmHubChromAlias.pl
@@ -152,31 +152,33 @@
 
 # foreach my $sequence (sort keys %chrNames) {
 #   printf "%s\t%s\n",  $chrNames{$sequence}, $sequence;
 # }
 
 ### next set of names are the equivalents declared by NCBI
 ### if they exist
 my %chr2acc;	# key is sequence name, value is NCBI chromosome name
 my $asmStructCount = `ls  ../../download/${asmId}_assembly_structure/*/*/chr2acc 2> /dev/null | wc -l`;
 chomp $asmStructCount;
 if ( $asmStructCount > 0 ) {
   printf STDERR "# second name set processing chr2acc files\n";
   open (FH, "grep -h -v '^#' ../../download/${asmId}_assembly_structure/*/*/chr2acc|") or die "can not grep chr2acc files";
   while (my $line = <FH>) {
     chomp $line;
-    my ($alias, $seqName) = split('\s+', $line);
+    my ($alias, $seqName) = split('\t', $line);
+    $alias =~ s/ /_/g;	# some assemblies have spaces in chr names ...
+    $alias =~ s/:/_/g;	# one assembly had : in a chr name
     $chr2acc{$seqName} = $alias;
     if ($ucscNames) {
        $seqName = $ncbiToUcsc{$seqName};
     }
     addAlias($alias, $seqName);
   }
   close (FH);
 }
 
 # foreach my $sequence (sort keys %chr2acc) {
 #   printf "%s\t%s\n",  $chr2acc{$sequence}, $sequence;
 # }
 
 my %gbk2acc;	# key is refseq name, value is genbank accession
 printf STDERR "# third set processing assembly_report\n";