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Christopher Fields > BioPerl > Bio::Tools::Coil



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Module Version: 1.007002   Source  


Bio::Tools::Coil - parser for Coil output


 use Bio::Tools::Coil
 my $parser = Bio::Tools::Coil->new();
 while( my $sp_feat = $parser->next_result($file) ) {
       #do something
       push @sp_feat, $sp_feat;


 Parser for Coil output


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 Based on the EnsEMBL module Bio::EnsEMBL::Pipeline::Runnable::Protein::Coil
 originally written by Marc Sohrmann (
 Written in BioPipe by Balamurugan Kumarasamy <>
# Please direct questions and support issues to <> 
 Cared for by the Fugu Informatics team (


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


 Title   : parse_results
 Usage   : obj->parse_results
 Function: Parses the coil output. Automatically called by
           next_result() if not yet done.
 Example :
 Returns :


 Title   : next_result
 Usage   : while($feat = $coil->next_result($file)) {
                  # do something
 Function: Returns the next protein feature of the coil output file
 Returns : 
 Args    :


 Title   : _result
 Usage   : $feat = $obj->_result()
 Function: internal
 Example :
 Returns :


 Title   : _add_prediction()
 Usage   : $obj->_add_prediction($feat)
 Function: internal
 Example :
 Returns :


 Title   : _predictions_parsed
 Usage   : $obj->_predictions_parsed
 Function: internal
 Example :
 Returns : TRUE or FALSE


 Title   : create_feature
 Usage   : obj->create_feature(\%feature)
 Function: Internal(not to be used directly)
 Returns :
 Args    :


 Title   : _read_fasta
 Usage   : obj->_read_fasta($file)
 Function: Internal(not to be used directly)
 Returns :
 Args    :
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