464d0311d4ec35f8ffe669e3ef75aa7f374ba926
hiram
  Mon Sep 21 17:44:51 2020 -0700
begin to work in the chromAlias construction to the assembly hubs refs #24396

diff --git src/hg/utils/automation/asmHubChromAlias.pl src/hg/utils/automation/asmHubChromAlias.pl
index 9147569..142fca7 100755
--- src/hg/utils/automation/asmHubChromAlias.pl
+++ src/hg/utils/automation/asmHubChromAlias.pl
@@ -1,161 +1,193 @@
 #!/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 %aliasOut;	# key is alias name, value is sequence name in this assembly
 
 sub showAlias() {
+printf "# sequenceName\talias names\n";
   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};
 #    printf "%s\t%s\n", $alias, $aliasOut{$alias};
     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;
 }
 
+##############################################################################
+########## experimental addVariations, not in use at this time ###############
+##############################################################################
 sub addVariations($$) {
   my ($alias, $sequence) = @_;
   addAlias($alias, $sequence);
   return;
-  addAlias(lc($alias), $sequence);
+
+  addAlias(lc($alias), $sequence);      # add lower case equivalent
   my $noDotName = $alias;
   $noDotName =~ s/\..*//;
-  addAlias($noDotName, $sequence);
-  addAlias(lc($noDotName), $sequence);
+  addAlias($noDotName, $sequence);      # add noDot name
+  addAlias(lc($noDotName), $sequence);  # and lower case noDot nae
   return;
 }
 
 my $asmId = shift;
 
+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 %sequenceNames;	# key is sequence name, value is sequence size
+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);
-  $sequenceNames{$name} = $size;
-  addVariations($name, $name);
+  $sequenceSizes{$name} = $size;
+  ++$sequenceCount;
 }
 
 close (FH);
 
-# foreach my $sequence (sort keys %sequenceNames) {
-#   printf "# %s\t%d\n", $sequence, $sequenceNames{$sequence};
-# }
-
-my %chrNames;	# key is sequence name, value is 'chr' UCSC chromosome name
+my $nameCount = 0;
+my %ncbiNames;	# key is NCBI sequence name, value is 'chr' UCSC chromosome name
+my %ucscNames;	# 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 $line;
-  my ($chr, $name) = split('\s+', $line);
-  $chrNames{$name} = $chr;
-  addVariations($chr, $name);
+  my ($ucscName, $seqName) = split('\s+', $line);
+  $ncbiNames{$seqName} = $ucscName;
+  $ucscNames{$ucscName} = $seqName;
+  ++$nameCount;
+  $ucscNames = 1 if (defined($sequenceSizes{$ucscName}));
+  if ($refSeq) {
+    $ucscToRefSeq{$ucscName} = $seqName;
+  } else {
+    $ucscToGenbank{$ucscName} = $seqName;
+  }
 }
 close (FH);
 
+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\n", $sequenceCount, $nameCount;
+  exit 255;
+}
+
+printf STDERR "# initial set with UCSC names\n";
+### first set of names is the UCSC to NCBI sequence names
+foreach my $sequence (sort keys %sequenceSizes) {
+  my $seqName = $sequence;
+  my $alias = $sequence;
+#   addVariations($seqName, $alias);      # obsolete identical usage
+  if ($ucscNames) {
+     $alias = $ucscNames{$seqName};
+  } else {
+     $alias = $ncbiNames{$seqName};
+  } 
+  if (!defined($alias)) {
+    printf STDERR "ERROR: can not find alias name for '%s' sequence\n", $seqName;
+    exit 255;
+  }
+  addVariations($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
-open (FH, "grep -h -v '^#' ../../download/${asmId}_assembly_structure/*/*/chr2acc|") or die "can not gep chr2acc files";
+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 $line;
-  my ($chr, $name) = split('\s+', $line);
-  $chr2acc{$name} = $chr;
-  addVariations($chr, $name);
+    my ($alias, $seqName) = split('\s+', $line);
+    $chr2acc{$seqName} = $alias;
+    if ($ucscNames) {
+       $seqName = $ncbiNames{$seqName};
+    }
+    addVariations($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 $line;
-  my ($gbk, $name) = split('\s+', $line);
-  next if ($name eq "na");	# may not be any RefSeq names
-  $gbk2acc{$name} = $gbk;
-  addVariations($gbk, $name);
+  my ($gbkName, $refSeqName) = split('\s+', $line);
+  next if ($refSeqName eq "na");	# may not be any RefSeq names
+  $gbk2acc{$gbkName} = $refSeqName;
+  if ($refSeq) {
+    my $seqName = $refSeqName;
+    if ($ucscNames) {
+       $seqName = $ncbiNames{$seqName};
+    }
+    addVariations($gbkName, $seqName);
+  } else {
+    my $seqName = $gbkName;
+    if ($ucscNames) {
+       $seqName = $ncbiNames{$seqName};
     }
-close (FH);
-
-showAlias();
-exit 0;
-
-foreach my $sequence (sort keys %gbk2acc) {
-  printf "%s\t%s\n",  $gbk2acc{$sequence}, $sequence;
+    addVariations($refSeqName, $seqName);
   }
-
-my %seq2gbk;	# key is genbank name, value is sequence name
-open (FH, "grep -v '^#' ../../download/${asmId}_assembly_report.txt | cut -d\$'\t' -f1,5|") or die "can not grep assembly_report";
-while (my $line = <FH>) {
-  chomp $line;
-  my ($seq, $name) = split('\s+', $line);
-  next if ($name eq "na");	# may not be any genbank name
-  $seq2gbk{$name} = $seq;
 }
 close (FH);
 
-foreach my $sequence (sort keys %seq2gbk) {
-  printf "%s\t%s\n",  $seq2gbk{$sequence}, $sequence;
-}
-
-__END__
-
-export asmId="GCF_000001735.4_TAIR10.1"
-
-grep -v "^#" ../../download/${asmId}_assembly_report.txt \
-  | cut -d$'\t' -f1,5
-
-grep -v "^#" ../../download/${asmId}_assembly_report.txt \
-  | cut -d$'\t' -f1,7
-
-grep -v "^#" ../../download/${asmId}_assembly_report.txt \
-  | cut -d$'\t' -f5,7
-
-2       assembled-molecule      2       Chromosome      CP002685.1      =      NC_003071.7      Primary Assembly        19698289        na
+showAlias();