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Bio::Tools::Coil.3pm

NAME

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

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:

   http://bugzilla.open-bio.org/
 
 

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    :