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

NAME

Bio::Tools::Run::Tmhmm - Object for identifying transmembrane helixes in a given protein seequence.

SYNOPSIS

# Build a Tmhmm  factory

# $paramfile is the full path to the seg binary file

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

# Pass the factory a Bio::Seq object
# @feats is an array of Bio::SeqFeature::Generic objects

my @feats = $factory->run($seq);

DESCRIPTION

Tmhmm is a program for identifying transmembrane helices in proteins.

You must have the environmental variable TMHMMDIR set to the base directory where tmhmm and it's associated data/option files reside (NOT the bin directory where the actual executable resides)

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

head2 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 - Bala

Email savikalpa@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, in this
          case it is the tmhmm installation directory, not the location of
          the executable.
Returns:  string
Args    :

program_path

Title   : program_path
Usage   : my $path = $factory->program_path();
Function: Builds path for executable 
Returns : string representing the full path to the exe
Args    : none

new

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

predict_protein_features

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

executable

Title   : executable
Usage   : my $exe = $tmhmm->executable('tmhmm');
Function: Finds the full path to the 'tmhmm' executable
Returns : string representing the full path to the exe
Args    : [optional] name of executable to set path to
          [optional] boolean flag whether or not warn when exe is not found

run

Title   :   run()
Usage   :   $obj->run($seq)
Function:   Runs Tmhmm and creates an array of featrues
Returns :   An array of Bio::SeqFeature::Generic objects
Args    :   A Bio::PrimarySeqI

_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    :