=head1 NAME
Bio::FeatureIO::interpro - read features from InterPro XML
=head1 SYNOPSIS
my $in = Bio::FeatureIO(-format=>'interpro');
while (my $feat = $in->next_feature) {
# do something with the Bio::SeqFeatureI object
}
=head1 DESCRIPTION
See L<http://www.ebi.ac.uk/interpro/documentation.html>.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:
http://bugzilla.open-bio.org/
=head1 AUTHOR - Allen Day
Email allenday@ucla.edu
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::FeatureIO::interpro;
use strict;
use base qw(Bio::FeatureIO);
use Bio::SeqFeature::Annotated;
use Bio::OntologyIO;
use Bio::Annotation::Comment;
use Bio::Annotation::DBLink;
use Bio::Annotation::OntologyTerm;
use Bio::Annotation::SimpleValue;
use Bio::Annotation::Target;
use URI::Escape;
use XML::DOM;
use XML::DOM::XPath;
sub _initialize {
my($self,%arg) = @_;
$self->SUPER::_initialize(%arg);
$self->xml_parser(XML::DOM::Parser->new());
my $buf;
while(($buf = $self->_readline()) && $buf !~ /<protein/){
next;
}
$self->_pushback($buf);
}
sub next_feature {
my $self =shift;
my $buf; #line buffer
my $ok = 0; #true if there is another <protein/> record in stream
my $record; #holds the record to be parsed and returned.
#try to dump buffer from last record before moving on to next record
my $f = $self->_shift_feature_buffer();
if($f){
return $f;
}
while(my $buf = $self->_readline()){
$ok = 1 if $buf =~ m!<protein!;
$record .= $buf;
last if $buf =~ m!</protein>!;
}
return unless $ok;
my $dom = $self->xml_parser->parse($record);
my ($pNode) = $dom->findnodes('/protein');
my @iNodes = $pNode->findnodes('/protein/interpro');
foreach my $iNode (@iNodes){
my @cNodes = $iNode->findnodes('classification');
my @mNodes = $iNode->findnodes('match');
#we don't handle these
#my @nNodes = $iNode->findnodes('contains');
#my @fNodes = $iNode->findnodes('found_in');
foreach my $mNode (@mNodes){
my @lNodes = $mNode->findnodes('location');
foreach my $lNode (@lNodes){
my $feature = Bio::SeqFeature::Annotated->new(
-start => $lNode->getAttribute('start'),
-end => $lNode->getAttribute('end'),
-score => $lNode->getAttribute('score'),
# -seq_id => $pNode->getAttribute('id'),
);
$feature->seq_id->value($pNode->getAttribute('id'));
#warn $pNode->getAttribute('id');
$feature->source( $lNode->getAttribute('evidence') );
my $t = Bio::Annotation::OntologyTerm->new(-identifier => 'SO:0000417', -name => 'polypeptide_domain');
$feature->add_Annotation('type',$t);
my $c = Bio::Annotation::Comment->new(-tagname => 'comment', -text => $iNode->getAttribute('name'));
$feature->add_Annotation($c);
my $d = Bio::Annotation::DBLink->new();
$d->database($mNode->getAttribute('dbname'));
$d->primary_id($mNode->getAttribute('id'));
$d->optional_id($mNode->getAttribute('name'));
$feature->annotation->add_Annotation('dblink',$d);
my $s = Bio::Annotation::SimpleValue->new(-tagname => 'status', -value => $lNode->getAttribute('status'));
$feature->annotation->add_Annotation($s);
foreach my $cNode (@cNodes){
my $o = Bio::Annotation::OntologyTerm->new(-identifier => $cNode->getAttribute('id'));
$feature->annotation->add_Annotation('ontology_term',$o);
}
$self->_push_feature_buffer($feature);
}
}
}
return $self->_shift_feature_buffer;
}
=head2 _push_feature_buffer()
Usage :
Function:
Returns :
Args :
=cut
sub _push_feature_buffer {
my ($self,$f) = @_;
if(ref($f)){
push @{ $self->{feature_buffer} }, $f;
}
}
=head2 _shift_feature_buffer()
Usage :
Function:
Returns :
Args :
=cut
sub _shift_feature_buffer {
my ($self) = @_;
return $self->{feature_buffer} ? shift @{ $self->{feature_buffer} } : undef;
}
=head2 xml_parser()
Usage : $obj->xml_parser($newval)
Function:
Example :
Returns : value of xml_parser (a scalar)
Args : on set, new value (a scalar or undef, optional)
=cut
sub xml_parser {
my($self,$val) = @_;
$self->{'xml_parser'} = $val if defined($val);
return $self->{'xml_parser'};
}
1;