Module associated with the Broad Magnaporthe Comparative DB; inherits fro mthe...

Module associated with the Broad Magnaporthe Comparative DB; inherits fro mthe generic broad parser, Broad_GenericParser.pm

misc-scripts/xref_mapping/XrefParser/Broad_MagnaportheDBParser.pm

+package XrefParser::Broad_MagnaportheDBParser;
+
+use strict;
+use warnings;
+use Carp;
+
+use base qw( XrefParser::Broad_GenericParser );
+
+sub run {
+
+    my ($self, $ref_arg) = @_;
+    my $source_id    = $ref_arg->{source_id};
+    my $species_id   = $ref_arg->{species_id};
+    my $files        = $ref_arg->{files};
+    my $verbose      = $ref_arg->{verbose};
+    
+    if((!defined $source_id) or (!defined $species_id) or (!defined $files) ){
+	croak "Need to pass source_id, species_id and  files as pairs";
+    }
+    $verbose |= 0;
+    
+    my $file = @{$files}[0];
+    
+    my $broad_source_id = $self->get_source_id_for_source_name("BROAD_Magnaporthe_DB");
+    $ref_arg->{source_id} = $broad_source_id;
+
+    # Parse the Broad gene summary file
+
+    my $xrefs_aref = $self->parse ($ref_arg);
+
+    # Store the parsed data as direct xrefs
+
+    my $errorcode = $self->store ($xrefs_aref);
+
+    return $errorcode;
+
+}
+
+1;
+