Bio::Tools::Run::TmhmmUser Contributed Perl DocumentaBio::Tools::Run::Tmhmm(3)NAMEBio::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://bugzilla.open-bio.org/
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 :
perl v5.14.1 2011-07-21 Bio::Tools::Run::Tmhmm(3)
