/ 
BioPerl-Run-1.007003
River stage one • 2 direct dependents • 2 total dependents
/ Bio::Tools::Run::Profile

NAME

Bio::Tools::Run::Profile

SYNOPSIS

Build a Profile factory
# $paramfile is the full path to the seg binary file

my @params = ('DB',$dbfile,'PROGRAM',$paramfile);
my $factory = Bio::Tools::Run::Profile->new($param);

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

DESCRIPTION

Wrapper module for the pfscan program

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://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 the bugs and their resolution. Bug reports can be submitted via the web:

http://redmine.open-bio.org/projects/bioperl/

AUTHOR - Balamurugan Kumarasamy

Email: fugui@worf.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, obtained from ENV variable.
Returns:  string
Args    :

new

Title   : new
Usage   : my $factory= Bio::Tools::Run::Profile->new($param);
Function: creates a new Profile factory
Returns:  Bio::Tools::Run::Profile
Args    :

predict_protein_features

Title   :   predict_protein_features
Usage   :   DEPRECATED. Use $factory->run($seq) instead.
Function:   Runs Profile and creates an array of featrues
Returns :   An array of L<Bio::SeqFeature::FeaturePair> objects
Args    :   A Bio::PrimarySeqI

run

Title   :   run
Usage   :   my @feats = $factory->run($seq)
Function:   Runs Profile 
Returns :   An array of L<Bio::SeqFeature::FeaturePair> objects
Args    :   A Bio::PrimarySeqI

_input

Title   :   _input
Usage   :   $factory->_input($seqFile)
Function:   get/set for input file
Returns :
Args    :

_run

Title   :   _run
Usage   :   $factory->_run()
Function:   Makes a system call and runs pfscan
Returns :   An array of L<Bio::SeqFeature::FeaturePair> objects
Args    :

_writeSeqFile

Title   :   _writeSeqFile
Usage   :   $factory->_writeSeqFile($seq)
Function:   Creates a file from the given seq object
Returns :   A string(filename) 
Args    :   Bio::PrimarySeqI