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
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 :