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Man Pages


Manual Reference Pages  -  BIO::TOOLS::COIL (3)

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NAME

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

CONTENTS

SYNOPSIS



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



DESCRIPTION



 Parser for Coil output



FEEDBACK

    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://github.com/bioperl/bioperl-live/issues



AUTHOR



 Based on the EnsEMBL module Bio::EnsEMBL::Pipeline::Runnable::Protein::Coil
 originally written by Marc Sohrmann (ms2@sanger.ac.uk)
 Written in BioPipe by Balamurugan Kumarasamy <savikalpa@fugu-sg.org>
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
 Cared for by the Fugu Informatics team (fuguteam@fugu-sg.org)



APPENDIX



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



    parse_results



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



    next_result



 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    :



    _result



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



    _add_prediction



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



    _predictions_parsed



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



    create_feature



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



    _read_fasta



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



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perl v5.20.3 BIO::TOOLS::COIL (3) 2016-04-05

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