Bio::FeatureIO interpro
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Summary
Bio::FeatureIO::interpro - read features from InterPro XML
Package variables
No package variables defined.
Included modules
Bio::Annotation::Comment
Bio::Annotation::DBLink
Bio::Annotation::OntologyTerm
Bio::Annotation::SimpleValue
Bio::Annotation::Target
Bio::OntologyIO
Bio::SeqFeature::Annotated
URI::Escape
XML::DOM
XML::DOM::XPath
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
_initialize
No description
Code
next_feature
No description
Code
_push_feature_bufferDescriptionCode
_shift_feature_bufferDescriptionCode
xml_parserDescriptionCode
Methods description
_push_feature_buffer()code    nextTop
 Usage   :
Function:
Returns :
Args :
_shift_feature_buffer()codeprevnextTop
 Usage   :
Function:
Returns :
Args :
xml_parser()codeprevnextTop
 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
_initializedescriptionprevnextTop
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);
}
next_featuredescriptionprevnextTop
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 $self->_shift_feature_buffer;
}
_push_feature_bufferdescriptionprevnextTop
sub _push_feature_buffer {
  my ($self,$f) = @_;

  if(ref($f)){
    push @{ $self->{feature_buffer} }, $f;
  }
}
_shift_feature_bufferdescriptionprevnextTop
sub _shift_feature_buffer {
  my ($self) = @_;
  return $self->{feature_buffer} ? shift @{ $self->{feature_buffer} } : undef;
}
xml_parserdescriptionprevnextTop
sub xml_parser {
  my($self,$val) = @_;
  $self->{'xml_parser'} = $val if defined($val);
  return $self->{'xml_parser'};
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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 DayTop
Email allenday@ucla.edu
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _