XrefParser::PomBaseParser Class Reference
Public Member Functions | |
| public | run () |
Detailed Description
Definition at line 5 of file PomBaseParser.pm.
Member Function Documentation
◆ run()
| public XrefParser::PomBaseParser::run | ( | ) |
Undocumented method
Code:
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sub run {
my ($self, $ref_arg) = @_;
my $source_id = $ref_arg->{source_id};
my $species_id = $ref_arg->{species_id};
my $files = $ref_arg->{files};
my $verbose = $ref_arg->{verbose};
my $dbi = $ref_arg->{dbi};
$dbi = $self->dbi unless defined $dbi;
if((!defined $source_id) or (!defined $species_id) or (!defined $files) ){
croak "Need to pass source_id, species_id and files as pairs";
}
$verbose |=0;
my $file = @{$files}[0];
my $gene_source_id = $self->get_source_id_for_source_name("PomBase_GENE", undef, $dbi);
my $transcript_source_id = $self->get_source_id_for_source_name("PomBase_TRANSCRIPT", undef, $dbi);
my $pombase_io = $self->get_filehandle($file);
if ( !defined $pombase_io ) {
print STDERR "ERROR: Could not open $file\n";
return 1; # 1 is an error
}
my $xref_count =0;
my $syn_count =0;
while ( $_ = $pombase_io->getline() ) {
chomp;
if ($_ =~ /^([^\t]+)\t([^\t]+)\t([^\t]*)\t([^\t]*)\t([^\t]*)\t([^\t]*)\t([^\t]*)\t([^\t]*)$/) {
my @line = split(m/\t/ms, $_);
my ($pombase_id, $name, $info_type, $biotype, $external_db_source, $desc, $ensembl_object_type, $synonyms) = undef;
$pombase_id = $line[0];
$name = $line[1];
$info_type = $line[2];
$biotype = $line[3];
$external_db_source = $line[4];
$desc = $line[5];
$ensembl_object_type = $line[6];
if (scalar @line == 8) {
$synonyms = $line[7];
}
# parse the lines corresponding to the gene entries
# and filter out lines corresponding to the CDS for example
#print "$ensembl_object_type\n";
if ($ensembl_object_type eq 'Gene') {
my $ensembl_xref_id = $self->add_xref({ acc => $pombase_id,
label => $name,
desc => $desc,
source_id => $gene_source_id,
species_id => $species_id,
dbi => $dbi,
info_type => $info_type} );
$self->add_direct_xref($ensembl_xref_id, $pombase_id, $ensembl_object_type, $info_type, $dbi);
} elsif ($ensembl_object_type eq 'Transcript') {
my $ensembl_xref_id = $self->add_xref({ acc => $pombase_id,
label => $name,
desc => $desc,
dbi => $dbi,
source_id => $transcript_source_id,
species_id => $species_id,
info_type => $info_type} );
$self->add_direct_xref($ensembl_xref_id, $pombase_id, $ensembl_object_type, $info_type, $dbi);
}
$xref_count++;
if ($synonyms) {
my (@syn) = split(/,/,$synonyms);
foreach my $synonym (@syn){
if ($verbose) {
print STDERR "adding synonym, $synonym\n";
}
$self->add_to_syn($pombase_id, $gene_source_id, $synonym, $species_id, $dbi);
$syn_count++;
}
}
} else {
if ($verbose) {
print STDERR "failed to parse line, $_\n\n";
}
}
}
$pombase_io->close();
print $xref_count." PomBase Xrefs added with $syn_count synonyms\n" if($verbose);
return 0; #successful
}
The documentation for this class was generated from the following file:
- ensembl/misc-scripts/xref_mapping/XrefParser/PomBaseParser.pm
