use methods in BaseParser now instead of local

misc-scripts/xref_mapping/XrefParser/MGDParser.pm

@@ -7,7 +7,7 @@ use File::Basename;
 use XrefParser::BaseParser;
  
 use vars qw(@ISA);
-@ISA = qw(BaseParser);
+@ISA = qw(XrefParser::BaseParser);
 
 my $xref_sth ;
 my $dep_sth;
@@ -36,30 +36,21 @@ sub run {
   my $source_id = shift;
   my $species_id = shift;
 
-  $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(?,?,?,?)");
-
-#  my $mrk_swiss = "MRK_SwissProt_TrEMBL.rpt";
-#  my $mrk_ll    = "MRK_LocusLink.rpt";
-
-#  my $dir =  dirname($file);  
-  
   if(!defined($source_id)){
-    $source_id = BaseParser->get_source_id_for_filename($file);
+    $source_id = XrefParser::BaseParser->get_source_id_for_filename($file);
     print "source id is $source_id \n";
   }
   if(!defined($species_id)){
-    $species_id = BaseParser->get_species_id_for_filename($file);
+    $species_id = XrefParser::BaseParser->get_species_id_for_filename($file);
     print "species id is $species_id \n";
   }                                                                                                                      
                                                                                                                       
-  my (%swiss) = BaseParser->get_valid_codes("uniprot",$species_id);
-  my (%refseq) = BaseParser->get_valid_codes("refseq",$species_id);
-
+  my (%swiss) = XrefParser::BaseParser->get_valid_codes("uniprot",$species_id);
+  my (%refseq) = XrefParser::BaseParser->get_valid_codes("refseq",$species_id);
 
-  print %swiss."\n";
 
+  my $count = 0;
+  my $mismatch = 0;
 
   open(FILE,"<". $file) || die "could not open file $file";
   while(my $line = <FILE>){
@@ -67,46 +58,32 @@ sub run {
     my ($key,$label,$sps) = (split("\t",$line))[0,1,6];
     my @sp = split(/\s/,$sps); 
     foreach my $value (@sp){
-#      print $value."\n";
       if(defined($value) and $value and defined($swiss{$value})){
-	add_to_xrefs($swiss{$value},$key,$label,$source_id,$species_id);
-
-#	print $key."\t".$value."\t".$label."\n";
+	XrefParser::BaseParser->add_to_xrefs($swiss{$value},$key,$label,"",$source_id,$species_id);
+	$count++;
       }
       elsif(defined($value) and $value and defined($refseq{$value})){
-	print STDERR "ARSE\t".$key."\t".$value."\t".$label."\n";	
+#	print STDERR "ARSE\t".$key."\t".$value."\t".$label."\n";	
+	$mismatch++;
       }
     }
   }
   close FILE;
+  print "$count xrefs succesfully loaded\n";
+  print "$mismatch xrefs failed to load\n";
      
 
 
 
 }                                                                                                                     
 
-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;
+sub new {
+
+  my $self = {};
+  bless $self, "XrefParser::MGDParser";
+  return $self;
+
 }
  
-sub add_to_xrefs{
-  my ($master_xref,$mgi,$label,$source_id,$species_id) = @_;
- 
-  my $dependent_id = get_xref($mgi, $source_id);
-  if(!defined($dependent_id)){
-    $xref_sth->execute($mgi,$label,"",$source_id,$species_id);
-  }
-  $dependent_id = get_xref($mgi, $source_id);
-  $dep_sth->execute($master_xref, $dependent_id,  "", $source_id);
- 
-}
+1;
+