HUGO parser. Ref seq Accesssion check still needs to be resolved as hugo has...

HUGO parser. Ref seq Accesssion check still needs to be resolved as hugo has NO version numbers whereas at the moment these are stored when parsing refseq

misc-scripts/xref_mapping/HUGOParser.pm

+package HUGOParser;
+  
+use strict;
+use POSIX qw(strftime);
+use File::Basename;
+  
+use BaseParser;
+  
+use vars qw(@ISA);
+@ISA = qw(BaseParser);
+ 
+my $xref_sth ;
+my $dep_sth;
+  
+ 
+  
+# --------------------------------------------------------------------------------
+# Parse command line and run if being run directly
+  
+if (!defined(caller())) {
+  
+  if (scalar(@ARGV) != 1) {
+    print "\nUsage: HUGOParser.pm file\n\n";
+    exit(1);
+  }
+  
+  run(@ARGV);
+}
+  
+ 
+sub run {
+  my $self = shift if (defined(caller(1)));
+  my $file = shift;
+ 
+  my $source_id = shift;
+  my $species_id = shift;
+
+  print STDERR $file."\n";
+  if(!defined($source_id)){
+    $source_id = BaseParser->get_source_id_for_filename($file);
+    print "source id is $source_id \n";
+  }
+  if(!defined($species_id)){
+    $species_id = BaseParser->get_species_id_for_filename($file);
+    print "species id is $species_id \n";
+  }
+
+  my $dir = dirname($file);
+ 
+  print STDERR $dir."\n";
+  
+  $xref_sth = BaseParser->dbi->prepare("INSERT INTO xref (accession,label,description,source_id,species_id) VALUES(?,?,?,?,?)");
+  $dep_sth = BaseParser->dbi->prepare("INSERT INTO dependent_xref VALUES(?,?,?,?)"); # xref1,xref2,"",hugo
+    
+
+  my %hugo;
+    
+  open (ENS4, $dir."/ens4.txt") || die "Can't open hugo ens4 $dir/ens4.txt\n";
+  #HGNC    Symbol  Literature Aliases      Withdrawn Symbols
+  #5       A1BG
+  #7       A2M
+  <ENS4>;  #header line
+  while(<ENS4>){
+    chomp;
+    my @array = split(/\t/,$_);
+    my $hgnc = $array[0];
+    my $label = $array[1];
+    
+    my $id = get_xref($hgnc, $source_id);
+    if(!defined($id)){
+      $xref_sth->execute($hgnc,$label,"",$source_id,$species_id);
+    }
+    $hugo{$hgnc} = get_xref($hgnc, $source_id);;
+  }
+  close ENS4;
+
+  
+  my (%swiss)  = BaseParser->get_valid_codes("uniprot",$species_id);
+  my (%refseq) = BaseParser->get_valid_codes("refseq",$species_id);
+  
+  open (ENS1, $dir."/ens1.txt") || die "Can't open hugo ens1  $dir/ens1.txt\n";
+  #HGNC    SWISSPROT       Ref Seq
+  #5       P04217  NM_130786
+  #7       P01023  NM_000014
+  <ENS1>;
+  while (<ENS1>) {
+    chomp;
+    my @array = split(/\t/,$_);
+    my $hgnc = $array[0];
+    
+    if ($array[1]) {  #swissprot
+      my $master = $swiss{$array[1]};
+      my $dep    = $hugo{$hgnc};
+      if(!defined($master) or !defined($dep)){
+	print STDERR $_."\n"; 
+	print STDERR "swiss prot $array[1] -> xref $master \n";
+	print STDERR "hugo number $hgnc -> xref $dep \n";
+      }
+      else{
+	$dep_sth->execute($master, $dep,  "", $source_id);
+      }
+      #	print "$array[1]\tSPTR\t$hgnc\tHUGO\t$hugo_id{$hgnc}\t$hugo_syn{$hgnc}\tXREF\n";
+    }
+    
+    if ($array[2]) {
+      my $master = $refseq{$array[2]};
+      my $dep    = $hugo{$hgnc};
+      if(!defined($master) or !defined($dep)){
+	print STDERR $_."\n"; 
+	print STDERR "ref seq $array[2] -> xref $master \n";
+	print STDERR "hugo number $hgnc -> xref $dep \n";
+      }
+      else{
+#	$dep_sth->execute($master, $dep,  "", $source_id);
+      }
+      #	print "$array[2]\tRefSeq\t$hgnc\tHUGO\t$hugo_id{$hgnc}\t$hugo_syn{$hgnc}\tXREF\n";
+    }
+  }
+  close (ENS1);
+  
+    
+}
+
+
+sub get_xref{
+  my ($acc,$source) = @_;
+  
+  my $dbi =BaseParser->dbi;
+  my $sql = "select xref_id from xref where accession = '".$acc."' and source_id = $source";
+  my $sth = $dbi->prepare($sql);
+    
+  $sth->execute() || die $dbi->errstr;
+  if(my @row = $sth->fetchrow_array()) {
+    return $row[0];
+  }
+  return undef;
+}
+  
+    
+