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

BioPerl documentation Contained in the BioPerl distribution.

Index

Code Index:

NAME

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

SYNOPSIS

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

DESCRIPTION

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

FEEDBACK

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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

Support

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.

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:

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

AUTHOR - Allen Day

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Email allenday@ucla.edu

APPENDIX

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

_push_feature_buffer()

 Usage   :
 Function:
 Returns : 
 Args    :

_shift_feature_buffer()

 Usage   :
 Function:
 Returns : 
 Args    :

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)
BioPerl documentation Contained in the BioPerl distribution. 

# 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;
}


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;