Work still needed on WormPepParser to add if not found and has a swissprot acc.

misc-scripts/xref_mapping/XrefParser/WormPepParser.pm

+package XrefParser::WormPepParser;
+
+use strict;
+use File::Basename;
+
+use XrefParser::BaseParser;
+
+use vars qw(@ISA);
+@ISA = qw(XrefParser::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: WormPepParser.pm file <source_id> <species_id>\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 "WORMPep source = $source_id\tspecies = $species_id\n";
+  if(!defined($source_id)){
+    $source_id = XrefParser::BaseParser->get_source_id_for_filename($file);
+  }
+  if(!defined($species_id)){
+    $species_id = XrefParser::BaseParser->get_species_id_for_filename($file);
+  }
+  my %worm = %{XrefParser::BaseParser->get_valid_xrefs_for_dependencies
+	      ('wormbase_transcript','Uniprot/SPTREMBL','RefSeq_peptide',
+	       'Uniprot/SWISSPROT')}; 
+  my $sql = "update xref set accession =\'?\' where xref_id=?";
+  my $dbi =  XrefParser::BaseParser->dbi();
+  my $sth = $dbi->prepare($sql);
+
+
+  my $count  = 0;
+
+  open(PEP,"<".$file) || die "Could not open $file\n";
+
+  while (<PEP>) {
+    my ($transcript, $wb, $swiss)  = (split(/\t/,substr($_,1)))[0,1,5];
+    
+    if($swiss =~ /SW:(.*)/){
+      $swiss = $1;
+    }
+#    else{
+#      print "ERR:".$_;
+#    }
+    if(length($wb) < 3){
+      print "ERRR:".$_;
+    }
+    
+    #Is the transcript different from the gene
+    my $diff =0;
+    my $gene;
+    if($transcript =~ /(\S+\.\d+)/){
+      $gene = $1;
+      if($gene ne $transcript){
+	$diff=1;
+      }
+    }
+    else{
+      die "Gene format not recognised $transcript\n";
+    }
+
+    my $exists =0;
+    # if gene stored as transcript so change this
+    if(defined($worm{$gene}) and !defined($worm{$transcript})){
+      # change accesion to transcript name instead of gene
+      $sth->execute($transcript, $worm{$gene}) || die $dbi->errstr;
+      print "changing $gene (".$worm{$gene}.") to $transcript\n";
+    }
+    # if no record exists for this 
+    elsif(!defined($worm{$gene}) and !defined($worm{$transcript})){
+      print "Could not find: $transcript  ????";
+      if($swiss){
+	print " on sw: $swiss";
+      }
+      print "\n";
+    }
+      
+
+#    print $gene,"\t",$swiss,"\t",$wb,"\n";
+  }
+#  die "Just testing at the moment\n";
+
+}
+
+  
+sub new {
+
+  my $self = {};
+  bless $self, "XrefParser::WormPepParser";
+  return $self;
+
+}
+
+1;
+