/ 
bioperl-run-1.4
/ Bio::Tools::Run::Coil

NAME

Bio::Tools::Run::Coil

SYNOPSIS

Build a Coil factory

my $factory = Bio::Tools::Run::Coil->new($params);

# Pass the factory a Bio::Seq object
# @feats is an array of Bio::SeqFeature::Generic objects
my @feats = $factory->run($seq);

DESCRIPTION

Wrapper module for Coil

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 one
of the Bioperl mailing lists.  Your participation is much appreciated.

bioperl-l@bioperl.org          - General discussion
http://bio.perl.org/MailList.html             - About the mailing lists

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.  Bug reports can be submitted via
email or the web:

bioperl-bugs@bioperl.org
http://bugzilla.bioperl.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>
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 _

program_name

Title   : program_name
Usage   : $factory>program_name()
Function: holds the program name 
Returns:  string 
Args    : None

program_dir

Title   : program_dir
Usage   : $factory->program_dir(@params)
Function: returns the program directory, obtiained from ENV variable. 
Returns:  string 
Args    :

new

Title   : new
Usage   : $coil->new(@params)
Function: creates a new Coil factory
Returns:  Bio::Tools::Run::Coil
Args    :

predict_protein_features

Title   :   predict_protein_features()
Usage   :   DEPRECATED. Use $obj->run instead. 
Function:   Runs Coil and creates an array of featrues
Returns :   An array of Bio::SeqFeature::Generic objects
Args    :   A Bio::PrimarySeqI

run

Title   :   run
Usage   :   $obj->run($seq)
Function:   Runs Coil and creates an array of featrues
Returns :   An array of Bio::SeqFeature::Generic objects
Args    :   A Bio::PrimarySeqI, or a Fasta filename.

_input

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

_run

Title   :   _run
Usage   :   $obj->_run()
Function:   Internal(not to be used directly)
Returns :   An array of Bio::SeqFeature::Generic objects
Args    :

_writeSeqFile

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