From f62a3d50d729466c1186fb45a9739ef7c8a83268 Mon Sep 17 00:00:00 2001
From: Rhoda Kinsella <rhoda@ebi.ac.uk>
Date: Fri, 25 Jul 2008 14:17:02 +0000
Subject: [PATCH] Parser for database of aberrant 3\' and 5\' splice sites
(DBASS)
---
.../xref_mapping/XrefParser/DBASSParser.pm | 82 +++++++++++++++++++
1 file changed, 82 insertions(+)
create mode 100644 misc-scripts/xref_mapping/XrefParser/DBASSParser.pm
diff --git a/misc-scripts/xref_mapping/XrefParser/DBASSParser.pm b/misc-scripts/xref_mapping/XrefParser/DBASSParser.pm
new file mode 100644
index 0000000000..14d0929d67
--- /dev/null
+++ b/misc-scripts/xref_mapping/XrefParser/DBASSParser.pm
@@ -0,0 +1,82 @@
+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;
--
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