Raw content of XrefParser::IPIParser
<![CDATA[package XrefParser::IPIParser;
use strict;
use File::Basename;
use base qw( XrefParser::BaseParser );
# IPI file format: fasta, e.g.
# >IPI:IPI00000005.1|SWISS-PROT:P01111|TREMBL:Q15104|REFSEQ_NP:NP_002515|ENSEMBL:ENSP00000261444 Tax_Id=9606 Transforming protein N-Ras
# 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 @xrefs;
local $/ = "\n>";
my $ipi_io = $self->get_filehandle($file);
if ( !defined $ipi_io ) {
print STDERR "ERROR: Could not open $file\n";
return 1; # 1 = error
}
my %species_tax_id = %{$self->get_taxonomy_from_species_id($species_id)};
while ( $_ = $ipi_io->getline() ) {
my $xref;
my ($header, $sequence) = $_ =~ /^>?(.+?)\n([^>]*)/s or warn("Can't parse FASTA entry: $_\n");
# deconstruct header
my @header = split /\|/, $header;
my ($ipi) = $header[0] =~ /^IPI:(IPI(\d)+(\.\d+)?)/ or warn("Can't deduce IPI identifier from " . $header[0]);
my ($ipi_ac, $ipi_ver) = $ipi =~ /(IPI\d+)\.(\d+)/;
my ($tax_id, $description) = $header[-1] =~ /.*Tax_Id=(\d+)\s+(.*)/;
# note currently we ignore all the other cross-references in the IPI file
# only interested in species with the taxonomy ID were looking for
next if ( !defined $tax_id || !defined $species_tax_id{$tax_id});
# make sequence into one long string
$sequence =~ s/\n//g;
# build the xref object and store it
$xref->{ACCESSION} = $ipi_ac;
$xref->{VERSION} = $ipi_ver;
$xref->{LABEL} = $ipi;
$xref->{DESCRIPTION} = $description;
$xref->{SEQUENCE} = $sequence;
$xref->{SOURCE_ID} = $source_id;
$xref->{SPECIES_ID} = $species_id;
$xref->{SEQUENCE_TYPE} = 'peptide';
$xref->{STATUS} = 'experimental';
$xref->{INFO_TYPE} = "SEQUENCE_MATCH";
push @xrefs, $xref;
}
$ipi_io->close();
XrefParser::BaseParser->upload_xref_object_graphs(\@xrefs);
print scalar(@xrefs) . " IPI xrefs succesfully parsed\n" if($verbose);
return 0; #successful
}
1;
]]>