From 11903754177ea5ffa840e01570b3b0b391691f60 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Mon, 12 Mar 2007 11:34:48 +0000
Subject: [PATCH] Add a parser for Vega fasta files.
---
.../xref_mapping/XrefParser/VegaParser.pm | 77 +++++++++++++++++++
1 file changed, 77 insertions(+)
create mode 100644 misc-scripts/xref_mapping/XrefParser/VegaParser.pm
diff --git a/misc-scripts/xref_mapping/XrefParser/VegaParser.pm b/misc-scripts/xref_mapping/XrefParser/VegaParser.pm
new file mode 100644
index 0000000000..e27e896791
--- /dev/null
+++ b/misc-scripts/xref_mapping/XrefParser/VegaParser.pm
@@ -0,0 +1,77 @@
+# $Id$
+
+package XrefParser::VegaParser;
+
+use warnings;
+use strict;
+
+use base qw( XrefParser::BaseParser );
+
+# Parses the Vega Fasta file format:
+#
+# >OTTMUSP00000002157 pep:known chromosome:VEGA:1:60690904:60717905:1 Gene:OTTMUSG00000002254 Transcript:OTTMUST00000004499
+# MTLRLLFLALNFFSVQVTENKILVKQSPLLVVDSNEVSLSCRYSYNLLAKEFRASLYKGV
+# NSDVEVCVGNGNFTYQPQFRSNAEFNCDGDFDNETVTFRLWNLHVNHTDIYFCKIEFMYP
+# PPYLDNERSNGTIIHIKEKHLCHTQSSPKLFWALVVVAGVLFCYGLLVTVALCVIWTNSR
+# RNRLLQSDYMNMTPRRPGLTRKPYQPYAPARDFAAYRP
+
+sub run
+{
+ my $self = shift;
+ my ( $source_id, $species_id, $file_name ) = @_;
+
+ my $file_io = $self->get_filehandle($file_name);
+
+ if ( !defined $file_io ) {
+ return 1; # Failed.
+ }
+
+ my @xrefs;
+ while ( defined( my $line = $file_io->getline() ) ) {
+ chomp $line;
+
+ if ( substr( $line, 0, 1 ) eq '>' ) {
+ # New sequence header.
+ my (
+ $vega_protein_id, $vega_type,
+ $vega_position, $vega_gene_id,
+ $vega_transcript_id
+ ) = split / /, $line;
+
+ substr( $vega_protein_id, 0, 1, '' ); # Remove initial '>',
+ substr( $vega_gene_id, 0, 5, '' ); # initial 'Gene:', and
+ substr( $vega_transcript_id, 0, 11, '' ); # 'Transcript:'.
+
+ my ( $vega_alphabet, $vega_status ) =
+ ( $vega_type =~ /(.*):(.*)/ );
+
+ my %xref = (
+ 'ACCESSION' => $vega_transcript_id,
+ 'LABEL' => $vega_transcript_id,
+ 'DESCRIPTION' =>
+ sprintf( "%s %s", $vega_type, $vega_position ),
+ 'SEQUENCE' => '',
+ 'SOURCE_ID' => $source_id,
+ 'SPECIES_ID' => $species_id,
+ 'SEQUENCE_TYPE' =>
+ ( $vega_alphabet eq 'pep' ? 'peptide' : 'dna' ),
+ 'STATUS' => $vega_status,
+ );
+
+ push @xrefs, \%xref;
+
+ } else {
+ $xrefs[-1]->{'SEQUENCE'} .= $line;
+ }
+ }
+
+ print scalar(@xrefs) . " Vega Fasta Xrefs successfully parsed\n";
+
+ $self->upload_xref_object_graphs( \@xrefs );
+
+ print "Done\n";
+
+ return 0; # Successful.
+}
+
+1;
--
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