Simplified since we're now using direct xrefs for elegans rather than mapping.

misc-scripts/xref_mapping/XrefParser/WormPepParser.pm

@@ -10,109 +10,52 @@ use vars qw(@ISA);
 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);
-  }
+# wormpep.table file format:
+#>B0025.1a	CE24759	vps-34	phosphatidylinositol 3-kinase	Confirmed	SW:Q9TXI7	AAF23184.1
+#>B0025.1b	CE24760	vps-34		Confirmed	SW:Q9TXI6	AAF23185.1
+#>B0025.1c	CE37691	vps-34		Confirmed	SW:Q5TYK9	AAV34807.1
 
-  run(@ARGV);
-}
+# Just need direct xref between B0025.1a (=stable ID for C. Elegans) and CE24759
 
 sub run {
 
-  my $self = shift if (defined(caller(1)));
-  my $file = shift;
-
-  my $source_id = shift;
-  my $species_id = shift;
+  my ($self, $file, $source_id, $species_id) = @_;
 
   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_source_id = XrefParser::BaseParser->get_source_id_for_source_name('wormbase_transcript');
 
-  my (%worm)  =  %{XrefParser::BaseParser->get_valid_codes("wormbase_transcript",$species_id)};
+  my $worm_source_id = XrefParser::BaseParser->get_source_id_for_source_name('wormpep_id');
 
-  my (%swiss)  =  %{XrefParser::BaseParser->get_valid_codes("Uniprot",$species_id)};
+  my $xref_sth = $self->dbi()->prepare("SELECT xref_id FROM xref WHERE accession=? AND source_id=$worm_source_id AND species_id=$species_id");
 
-  my $sql = "update xref set accession =? where xref_id=?";
-  my $dbi =  XrefParser::BaseParser->dbi();
-  my $sth = $dbi->prepare($sql);
+  open(PEP,"<".$file) || die "Could not open $file\n";
 
+  my ($x_count, $d_count);
 
-  my $sql2 = "select x2.accession, x2.xref_id ";
-  $sql2   .= "from dependent_xref d, xref x1, xref x2 ";
-  $sql2   .= "where d.master_xref_id = x1.xref_id and ";
-  $sql2   .= "      d.dependent_xref_id = x2.xref_id and ";
-  $sql2   .= "      x2.source_id = $worm_source_id and ";
-  $sql2   .= "      x1.xref_id = ? and ";
-  $sql2   .= "      x2.accession = ?";
-  my $sth2 = $dbi->prepare($sql2);
+  while (<PEP>) {
 
+    my ($transcript, $wb)  = (split(/\t/,substr($_,1)))[0,1];
 
-  my $sql3 = 'delete from dependent_xref where dependent_xref.master_xref_id=? and dependent_xref.dependent_xref_id=?'; 
-  my $sth3 = $dbi->prepare($sql3);
+    # reuse or create xref
+    my $xref_id;
+    $xref_sth->execute($wb);
+    my $xref_id = ($xref_sth->fetchrow_array())[0];
+    if (!$xref_id) {
+      $xref_id = $self->add_xref($wb, undef, $wb, "", $worm_source_id, $species_id);
+      $x_count++;
+    }
 
-  open(PEP,"<".$file) || die "Could not open $file\n";
+    # and direct xref
+    $self->add_direct_xref($xref_id, $transcript, "transcript", "");
 
-  while (<PEP>) {
-    my ($transcript, $wb, $swiss_ref)  = (split(/\t/,substr($_,1)))[0,1,5];
-    my $swiss_xref;
-    if($swiss_ref =~ /SW:(.*)/){
-      $swiss_ref = $1;
-      if(defined($swiss{$swiss_ref})){
-	$swiss_xref = $swiss{$swiss_ref};
-	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";
-	}
-
-	$sth2->execute($swiss_xref, $gene) || die $dbi->errstr;
-	(my $gene_acc, my $gene_xref) = $sth2->fetchrow_array();
-
-	$sth2->execute($swiss_xref, $transcript) || die $dbi->errstr;
-	(my $tran_acc, my $tran_xref) =  $sth2->fetchrow_array();
-
-	my $create = 1;
-	if(defined($tran_xref)){ #okay
-	  $create = 0;
-	}
-	elsif(defined($gene_xref)){
-	  #need to delete dependency
-	  #then add new one with correct name
-	  $sth3->execute($swiss_xref, $gene_xref) || die $dbi->errstr;
-	  print "removing $swiss_ref -> $gene : ";
-	}
-	if($create){
-	  XrefParser::BaseParser->add_to_xrefs($swiss_xref,$transcript,'',$transcript,"","",$worm_source_id,$species_id);	  
-	  print "adding $swiss_ref -> $transcript\n";
-	}
-	
-      }
-      
-    }
+    $d_count++;
   }
-  
+
+  close (PEP);
+
+  print "Added $d_count direct xrefs and $x_count xrefs\n";
+
 }
 
-  
 sub new {
 
   my $self = {};