XrefParser MGDParser
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Package variables
Privates (from "my" definitions)
$xref_sth ;
$dep_sth;
Included modules
File::Basename
POSIX qw ( strftime )
Inherit
XrefParser::BaseParser
Synopsis
No synopsis!
Description
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Methods
run
No description
Code
Methods description
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Methods code
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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;
  $verbose       = shift;

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

  die "No longer used. MGI is taken form the uniprot file\n";

  if(!defined($source_id)){
    $source_id = XrefParser::BaseParser->get_source_id_for_filename($file);
  }
  if(!defined($species_id)){
    $species_id = XrefParser::BaseParser->get_species_id_for_filename($file);
  }                                                                                                                      
                                                                                                                      
  my (%swiss) = %{XrefParser::BaseParser->get_valid_codes("uniprot",$species_id)};
  my (%refseq) = %{XrefParser::BaseParser->get_valid_codes("refseq",$species_id)};


  my $count = 0;
  my $mismatch = 0;
  my %mgi_good;

  my $file_io = $self->get_filehandle($file);

  if ( !defined $file_io ) {
    print "ERROR: Could not open file $file";
    return 1;    # 1 is an error
} while ( my $line = $file_io->getline() ) { chomp $line; my ($key,$label,$desc,$sps) = (split("\t",$line))[0,1,3,6]; my @sp = split(/\s/,$sps); foreach my $value (@sp){ if(defined($value) and $value and defined($swiss{$value})){ XrefParser::BaseParser->add_to_xrefs($swiss{$value},$key,'',$label,$desc,"",$source_id,$species_id); $mgi_good{$key} = 1; $count++; } elsif(defined($value) and $value and defined($refseq{$value})){ $mismatch++; } } } $file_io->close(); my $dir = dirname($file); my $syn_file = $dir."/MRK_Synonym.sql.rpt"; $file_io = $self->get_filehandle($syn_file); if ( !defined $file_io ) { print "ERROR: Could not open file $syn_file"; return 1; } my $synonyms=0; while ( $_ = $file_io->getline() ) { if(/MGI:/){ chomp ; my ($key,$syn) = (split)[0,4]; if(defined($mgi_good{$key})){ $self->add_to_syn($key, $source_id, $syn, $species_id); $synonyms++; } } } $file_io->close(); print "\t$count xrefs succesfully loaded\n"; print "\t$synonyms synonyms successfully loaded\n"; print "\t$mismatch xrefs failed to load\n"; return 0; } 1;
}
General documentation
No general documentation available.