my ($self, $ref_arg) = @_;
my $source_id = $ref_arg->{source_id};
my $species_id = $ref_arg->{species_id};
my $files = $ref_arg->{files};
my $release_file = $ref_arg->{rel_file};
my $verbose = $ref_arg->{verbose};
if((!defined $source_id) or (!defined $species_id) or (!defined $files) or (!defined $release_file)){
croak "Need to pass source_id, species_id, files and rel_file as pairs";
}
$verbose |=0;
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
# 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();
$self->upload_xref_object_graphs(\@xrefs);
print scalar(@xrefs) . " Codelink xrefs succesfully parsed\n" if($verbose);
return 0; #successful
}
Code:
