no longer used. just confusing having it here

misc-scripts/xref_mapping/XrefParser/VegaParser.pm

-# $Id$
-
-package XrefParser::VegaParser;
-
-use warnings;
-use strict;
-
-use base qw( XrefParser::BaseParser );
-
-# Parses the Vega CDNA and Peptide Fasta file format:
-#
-# >OTTMUST00000004500 cdna:tot chromosome:VEGA:1:60690948:60709172:1 Gene:OTTMUSG00000002254
-# GTGACTTCAGTTCACACCACACTCTGCCTTGCTCACAGAGGAGGGGCTGCAGCCCTGGCC
-# CTCATCAGAACAATGACACTCAGGCTGCTGTTCTTGGCTCTCAACTTCTTCTCAGTTCAA
-# GTAACAGAAAACAAGATTTTGGTAAAGCAGTCGCCCCTGCTTGTGGTAGATAGCAACGAG
-#
-# >OTTMUSP00000002157 pep:known chromosome:VEGA:1:60690904:60717905:1 Gene:OTTMUSG00000002254 Transcript:OTTMUST00000004499
-# MTLRLLFLALNFFSVQVTENKILVKQSPLLVVDSNEVSLSCRYSYNLLAKEFRASLYKGV
-# NSDVEVCVGNGNFTYQPQFRSNAEFNCDGDFDNETVTFRLWNLHVNHTDIYFCKIEFMYP
-# PPYLDNERSNGTIIHIKEKHLCHTQSSPKLFWALVVVAGVLFCYGLLVTVALCVIWTNSR
-# RNRLLQSDYMNMTPRRPGLTRKPYQPYAPARDFAAYRP
-
-sub run
-{
-  my $self = shift if (defined(caller(1)));
-
-  my $source_id = shift;
-  my $species_id = shift;
-  my $files_ref  = shift;
-  my $rel_file   = shift;
-  my $verbose = shift;
-  
-  my $file_name = @{$files_ref}[0];
-  
-  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.
-
-            substr( $line, 0, 1, '' );    # Remove initial '>'
-
-            my ( $vega_id, $vega_alphabet ) =
-              ( $line =~ /^(\S+)\s([^:]+):/ );
-
-            my %xref = (
-                'ACCESSION'   => $vega_id,
-                'LABEL'       => $vega_id,
-                'DESCRIPTION' => $line,
-                'SEQUENCE'    => '',
-                'SOURCE_ID'   => $source_id,
-                'SPECIES_ID'  => $species_id,
-                'SEQUENCE_TYPE' =>
-                  ( $vega_alphabet eq 'pep' ? 'peptide' : 'dna' ),
-                'STATUS' => 'experimental'
-            );
-
-            push @xrefs, \%xref;
-
-        } else {
-            $xrefs[-1]->{'SEQUENCE'} .= $line;
-        }
-    }
-
-
-    $self->upload_xref_object_graphs( \@xrefs );
-
-    print scalar(@xrefs) . " Vega Fasta Xrefs successfully parsed\n" if($verbose);
-
-    return 0;    # Successful.
-}
-
-1;