Reference

Bio::Tools::Coil(3pm)

parser for Coil output

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.
  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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 ([email protected])
 Written in BioPipe by Balamurugan Kumarasamy <[email protected]>
# Please direct questions and support issues to <[email protected]> 
#
 Cared for by the Fugu Informatics team ([email protected])

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    :

History