Raw content of XrefParser::XenopusJamboreeParser
<![CDATA[package XrefParser::XenopusJamboreeParser;
# Parse annotated peptides from Xenopus Jamboree
use strict;
use File::Basename;
use base qw( XrefParser::BaseParser );
# Xenopus Jamboree peptides file format: fasta, e.g.
# >anxa2 BC061610
# MSLIHEILGKLSLEGNQSSTRQSTLGSVKASSNFDAERDAAAIETAIKTKGVDELTII
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 @xrefs;
local $/ = "\n>";
my $file_io = $self->getline($file);
if ( !defined $file_io ) {
print STDERR "ERROR: Could not open $file\n";
return 1; # 1 error
}
while ( $_ = $file_io->getline() ) {
my $xref;
my ($header, $sequence) = $_ =~ /^>?(.+?)\n([^>]*)/s or warn("Can't parse FASTA entry: $_\n");
# deconstruct header
my ($accession, @other) = split /\s+/, $header;
my $other = join(" ", @other);
# make sequence into one long string
$sequence =~ s/\n//g;
# build the xref object and store it
$xref->{ACCESSION} = $accession;
$xref->{LABEL} = $accession;
$xref->{DESCRIPTION} = '';
$xref->{SEQUENCE} = $sequence;
$xref->{SOURCE_ID} = $source_id;
$xref->{SPECIES_ID} = $species_id;
$xref->{SEQUENCE_TYPE} = 'peptide';
$xref->{STATUS} = 'experimental';
push @xrefs, $xref;
}
$file_io->close();
print scalar(@xrefs) . " XenopusJamboreeParser xrefs succesfully parsed\n" if($verbose);
if(!defined(XrefParser::BaseParser->upload_xref_object_graphs(\@xrefs))){
return 1; #1 error
}
return 0;
}
1;
]]>