Parser for database of aberrant 3\' and 5\' splice sites (DBASS)

misc-scripts/xref_mapping/XrefParser/DBASSParser.pm

+package XrefParser::DBASSParser;
+
+use strict;
+
+use base qw( XrefParser::BaseParser);
+
+# This parser will read direct xrefs from a simple comma-delimited file downloaded from the DBASS database.
+# The columns of the file should be the following:
+#
+# 1)    DBASS Gene ID
+# 2)    DBASS Gene Name
+# 3)    Ensembl Gene ID
+
+
+sub new {
+    my $proto = shift;
+
+    my $class = ref $proto || $proto;
+    my $self = bless {}, $class;
+
+    return $self;
+}
+
+sub run {
+    my $self = shift;
+
+    my ( $source_id, $species_id, $filename ) = @_;
+
+    my $file_io = $self->get_filehandle($filename);
+    if ( !defined($file_io) ) {
+        return 1;
+    }
+
+    my $parsed_count = 0;
+
+    printf( STDERR "source = %d\t species = %d\n",
+            $source_id, $species_id );
+
+    $file_io->getline();
+    
+    while ( defined( my $line = $file_io->getline() ) ) {
+ 
+	$line =~ s/\s*$//;
+		
+
+        my ( $dbass_gene_id, $dbass_gene_name, $ensembl_id) = split( /,/, $line );
+
+        if ( !defined($dbass_gene_id) || !defined($ensembl_id) ) {
+            printf( "Line %d contains  has less than two columns.\n",
+                    1 + $parsed_count );
+            print ("The parsing failed\n");
+            return 1;
+        }
+	
+        my $label       = $dbass_gene_name;
+	my $type        = 'gene';
+        my $description = '';
+        my $version     = '1';
+
+        ++$parsed_count;
+
+        my $xref_id = XrefParser::BaseParser->get_xref( $dbass_gene_id, $source_id );
+
+        if ( !defined($xref_id) || $xref_id eq '' ) {
+            $xref_id = XrefParser::BaseParser->add_xref($dbass_gene_id, $version, $label, $description, $source_id, $species_id);
+        }
+	
+	
+	XrefParser::BaseParser->add_direct_xref( $xref_id, $ensembl_id, $type, $dbass_gene_id);
+	
+    } ## end while ( defined( my $line...
+
+    printf( "%d direct xrefs succesfully parsed\n", $parsed_count );
+
+    $file_io->close();
+
+    print "Done\n";
+
+    return 0;
+} ## end sub run
+
+1;