XrefParser CodelinkParser
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File::Basename
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XrefParser::BaseParser
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run
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sub run {
  my $self = shift if (defined(caller(1)));

  my $source_id = shift;
  my $species_id = shift;
  my $files       = shift;
  my $release_file   = shift;
  my $verbose       = shift;

  my $file = @{$files}[0];

  my @xrefs;

  local $/ = "\n>";

  my $codelink_io = $self->get_filehandle($file);
  if ( !defined $codelink_io ) {
    print STDERR "ERROR: Could not open $file\n";
    return 1;    # 1 = error
} while ( $_ = $codelink_io->getline() ) { my $xref; my ($header, $sequence) = $_ =~ /^>?(.+?)\n([^>]*)/s or warn("Can't parse FASTA entry: $_\n"); # deconstruct header - only accession for now
my $accession = $header; # make sequence into one long string - probably not necessary for short probes
$sequence =~ s/\n//g; # build the xref object and store it
$xref->{ACCESSION} = $accession; $xref->{LABEL} = $accession; $xref->{SEQUENCE} = $sequence; $xref->{SOURCE_ID} = $source_id; $xref->{SPECIES_ID} = $species_id; $xref->{SEQUENCE_TYPE} = 'dna'; $xref->{STATUS} = 'experimental'; push @xrefs, $xref; } $codelink_io->close(); XrefParser::BaseParser->upload_xref_object_graphs(\@xrefs); print scalar(@xrefs) . " Codelink xrefs succesfully parsed\n" if($verbose); return 0; #successful
} 1;
}
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