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Summary

Bio::FeatureIO::interpro - read features from InterPro XML

Package variables

Included modules

Inherit

Bio::FeatureIO

Synopsis

  my $in = Bio::FeatureIO(-format=>'interpro');
  while (my $feat = $in->next_feature) {
    # do something with the Bio::SeqFeatureI object
  }

Description

See http://www.ebi.ac.uk/interpro/documentation.html.

Methods

Methods description

 Usage   :
 Function:
 Returns : 
 Args    :

 Usage   :
 Function:
 Returns : 
 Args    :

 Usage   : $obj->xml_parser($newval)
 Function: 
 Example : 
 Returns : value of xml_parser (a scalar)
 Args    : on set, new value (a scalar or undef, optional)

Methods code

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;

}

sub _push_feature_buffer {

  my ($self,$f) = @_;

  if(ref($f)){
    push @{ $self->{feature_buffer} }, $f;
  }

}

sub _shift_feature_buffer {

  my ($self) = @_;
  return $self->{feature_buffer} ? shift @{ $self->{feature_buffer} } : undef;

}

sub xml_parser {

  my($self,$val) = @_;
  $self->{'xml_parser'} = $val if defined($val);
  return $self->{'xml_parser'};
}

1;

}

General documentation

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

Please direct usage questions or support issues to the mailing list:
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.

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:

  https://redmine.open-bio.org/projects/bioperl/

Email allenday@ucla.edu

The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _