UniProtParser.pm

# Parse UniProt (SwissProt & SPTrEMBL) files to create xrefs.
#
# Files actually contain both types of xref, distinguished by ID line;
#
# ID   CYC_PIG                 Reviewed;         104 AA.  Swissprot
# ID   Q3ASY8_CHLCH            Unreviewed;     36805 AA.  SPTrEMBL



package XrefParser::UniProtParser;

use strict;
use POSIX qw(strftime);
use File::Basename;

use base qw( XrefParser::BaseParser );


my $verbose;

# --------------------------------------------------------------------------------
# Parse command line and run if being run directly

if (!defined(caller())) {

  if (scalar(@ARGV) != 3) {
    print STDERR "\nUsage: UniProtParser.pm file.SPC <source_id> <species_id>\n\n";
    print STDERR scalar(@ARGV);
    exit(1);
  }

  run($ARGV[0], -1);

}

# --------------------------------------------------------------------------------


sub run {

  my $self = shift if (defined(caller(1)));

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

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

  my $species_name;

  my ( $sp_source_id, $sptr_source_id, $sp_release, $sptr_release );

  if(!defined($species_id)){
    ($species_id, $species_name) = $self->get_species($file);
  }

  $sp_source_id =
    $self->get_source_id_for_source_name('Uniprot/SWISSPROT',"sequence_mapped");
  $sptr_source_id =
    $self->get_source_id_for_source_name('Uniprot/SPTREMBL');

  print "SwissProt source id for $file: $sp_source_id\n" if ($verbose);
  print "SpTREMBL source id for $file: $sptr_source_id\n" if ($verbose);
 

  my @xrefs =
    $self->create_xrefs( $sp_source_id, $sptr_source_id, $species_id,
      $file );