be4311c07e14feb728abc6425ee606ffaa611a58
markd
  Fri Jan 22 06:46:58 2021 -0800
merge with master

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
@@ -1,225 +1,227 @@
 #!/usr/bin/env perl
 
 use strict;
 use warnings;
 
 my $argc = scalar(@ARGV);
 if ($argc != 1) {
   printf STDERR "usage: asmHubChromAlias.pl asmId > asmId.chromAlias.tab\n\n";
   printf STDERR "where asmId is something like: GCF_000001735.4_TAIR10.1\n";
   printf STDERR "Outputs a tab file suitable for processing with ixIxx to\n";
   printf STDERR "create an index file to use in an assembly hub.\n";
   printf STDERR "This command assumes it is in a work directory in the\n";
   printf STDERR "assembly hub: .../asmId/trackData/chromAlias/\n";
   printf STDERR "and .../asmId/downloads/ and .../asmId/sequence/ have\n";
   printf STDERR "been created and processed for the hub build.\n";
   exit 255;
 }
 
 my %ucscToRefSeq;	# key is UCSC sequence name, value is RefSeq name
 my %ucscToGenbank;	# key is UCSC sequence name, value is GenBank name
 my $ucscNames = 0;	# == 1 if sequence is UCSC names, == 0 if NCBI names
 my $dupCount = 0;
 my %dupToSequence;	# key is duplicate name, value is target sequence name
 			# to manage duplicates coming in from assembly report
 
 my $asmId = shift;
 
 my %aliasOut;	# key is alias name, value is sequence name in this assembly
 
 sub showAlias() {
   printf "# sequenceName\talias names\tassembly: %s\n", $asmId;
   my %chromIndex;	# key is sequence name in assembly, value
                         # is a tab separated list of aliases
   foreach my $alias (sort keys %aliasOut) {
     my $name = $aliasOut{$alias};
     next if ($alias eq "na");
     if (defined($chromIndex{$name})) {
       $chromIndex{$name} .= "\t" . $alias;
     } else {
       $chromIndex{$name} = $alias;
     }
   }
   foreach my $name (sort keys %chromIndex) {
     printf "%s\t%s\n", $name, $chromIndex{$name};
   }
 }
 
 #  given an alias and a sequence name, add to result or verify identical
 #  to previous add
 sub addAlias($$) {
   my ($alias, $sequence) = @_;
   # do not need to add the sequence name itself
   return if ($alias eq $sequence);
   # already done, verify it is equivalent to previous request
   if (defined($aliasOut{$alias})) {
      if ($sequence ne $aliasOut{$alias}) {
         printf STDERR "ERROR: additional alias '%s:%s' does not match previous '%s'\n", $alias, $sequence, $aliasOut{$alias};
         exit 255;
      }
      return;
   }
   $aliasOut{$alias} = $sequence;
   return;
 }
 
 my $refSeq = 0; #       == 0 for Genbank assembly, == 1 for RefSeq assembly
 $refSeq = 1 if ($asmId =~ m/^GCF/);
 
 my $twoBit = "../../$asmId.2bit";
 my $sequenceCount = 0;
 my %sequenceSizes;	# key is sequence name, value is sequence size
 
 open (FH, "twoBitInfo $twoBit stdout|") or die "can not twoBitInfo $twoBit stdout";
 while (my $line = <FH>) {
   chomp $line;
   my ($name, $size) = split('\s+', $line);
   $sequenceSizes{$name} = $size;
   ++$sequenceCount;
 }
 
 close (FH);
 
 my $nameCount = 0;
 my %ncbiToUcsc;	# key is NCBI sequence name, value is 'chr' UCSC chromosome name
 my %ucscToNcbi;	# key is 'chr' UCSC name, value is NCBI sequence name
 open (FH, "cat ../../sequence/*.names|") or die "can not cat ../../sequence/*.names";
 while (my $line = <FH>) {
   chomp $line;
   my ($ucscName, $seqName) = split('\s+', $line);
   $ncbiToUcsc{$seqName} = $ucscName;
   $ucscToNcbi{$ucscName} = $seqName;
   ++$nameCount;
   $ucscNames = 1 if (defined($sequenceSizes{$ucscName}));
   if ($refSeq) {
     $ucscToRefSeq{$ucscName} = $seqName;
   } else {
     $ucscToGenbank{$ucscName} = $seqName;
   }
 }
 close (FH);
 
 my $dupsNotFound = 0;
 my $dupsList = "../../download/$asmId.dups.txt.gz";
 if ( -s "$dupsList" ) {
   open (FH, "zcat $dupsList | awk '{print \$1, \$3}'|") or die "can not read $dupsList";
   while (my $line = <FH>) {
     chomp $line;
     my ($dupAlias, $dupTarget) = split('\s+', $line);
     $dupToSequence{$dupAlias} = $dupTarget;
     if ($ucscNames) {
       if (!defined($ncbiToUcsc{$dupTarget})) {
        printf STDERR "# ERROR: can not find dupTarget: $dupTarget in ncbiToUcsc for dupAlias: $dupAlias\n";
          $dupsNotFound += 1;
       } else {
         addAlias($dupAlias, $ncbiToUcsc{$dupTarget});
       }
     } else {
         addAlias($dupAlias, $dupTarget);
     }
     ++$dupCount;
   }
   close (FH);
 }
 
 if ($dupsNotFound > 0) {
   printf STDERR "ERROR: can not find %d duplicate names\n", $dupsNotFound;
   exit 255;
 }
 
 if ($sequenceCount != $nameCount) {
   printf STDERR "ERROR: do not find the same name count in sequence vs. names files\n";
   printf STDERR "sequenceCount %d != %d names count - %d duplicates\n", $sequenceCount, $nameCount, $dupCount;
   exit 255;
 }
 
 printf STDERR "# initial set of %d UCSC names\n", $sequenceCount;
 ### first set of names is the UCSC to NCBI sequence names
 foreach my $sequence (sort keys %sequenceSizes) {
   my $seqName = $sequence;
   my $alias = $sequence;
   if ($ucscNames) {
      $alias = $ucscToNcbi{$seqName};
   } else {
      $alias = $ncbiToUcsc{$seqName};
   } 
   if (!defined($alias)) {
     printf STDERR "ERROR: can not find alias name for '%s' sequence\n", $seqName;
     exit 255;
   }
   addAlias($alias, $seqName);
 }
 
 # 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";
 # column 5 is the GenBank-Accn, column 7 is the RefSeq-Accn
 open (FH, "grep -v '^#' ../../download/${asmId}_assembly_report.txt | cut -d\$'\t' -f5,7|") or die "can not grep assembly_report";
 while (my $line = <FH>) {
   chomp $line;
   my ($gbkName, $refSeqName) = split('\s+', $line);
   next if ($refSeqName eq "na");	# may not be any RefSeq name
   next if ($gbkName eq "na");	# may not be any GenBank name
   $gbk2acc{$gbkName} = $refSeqName;
   if ($refSeq) {
     my $seqName = $refSeqName;
     if ($ucscNames) {
        $seqName = $ncbiToUcsc{$seqName};
     }
     if (!defined($seqName)) {
        if (defined($aliasOut{$refSeqName})) {
           $seqName = $aliasOut{$refSeqName};
        }
     }
     if ($dupToSequence{$seqName}) {
       addAlias($gbkName, $dupToSequence{$seqName});
     } else {
       addAlias($gbkName, $seqName);
     }
   } else {
     my $seqName = $gbkName;
     if ($ucscNames) {
        $seqName = $ncbiToUcsc{$seqName};
     }
     if (!defined($seqName)) {
        if (defined($aliasOut{$gbkName})) {
           $seqName = $aliasOut{$gbkName};
        }
     }
     if ($dupToSequence{$seqName}) {
       addAlias($refSeqName, $dupToSequence{$seqName});
     } else {
       addAlias($refSeqName, $seqName);
     }
   }
 }
 close (FH);
 
 showAlias();