Raw content of XrefParser::FastaParser
<![CDATA[package XrefParser::FastaParser;
use strict;
use Bio::SeqIO;
use File::Basename;
use base qw( XrefParser::BaseParser );
# Fasta file format, e.g.
# >foo peptide sequence for the foo gene
# MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAG
# PTRTVDTKQAHELAKSYGIPFIETSAKTRQGVEDAFYTLVREIRQYRMKKLNSSDDGTQG
# CMGLPCVVM
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 $sio = Bio::SeqIO->new(-format=>'fasta' , -file=>$file );
my %species_tax_id = %{$self->get_taxonomy_from_species_id($species_id)};
my @xrefs;
while( my $seq = $sio->next_seq ) {
# Test species if available
if( my $sp = $seq->species ){
if( my $tax_id = $sp->ncbi_taxid ){
next if (!defined $species_tax_id{$tax_id});
}
}
# build the xref object and store it
my $xref;
$xref->{ACCESSION} = $seq->display_name;
$xref->{LABEL} = $seq->display_name;
$xref->{DESCRIPTION} = $seq->description;
$xref->{SEQUENCE} = $seq->seq;
$xref->{SOURCE_ID} = $source_id;
$xref->{SPECIES_ID} = $species_id;
$xref->{SEQUENCE_TYPE} = $seq->alphabet eq 'protein' ? 'peptide' : 'dna';
$xref->{STATUS} = 'experimental';
if( my $v = $seq->version ){ $xref->{VERSION} = $v };
push @xrefs, $xref;
}
print scalar(@xrefs) . " Fasta xrefs succesfully parsed\n" if($verbose);
$self->upload_xref_object_graphs(\@xrefs);
print scalar(@xrefs) . " Fasta xrefs succesfully loaded\n" if($verbose);
return 0; #successful
}
1;
]]>