Bio::Tools::Run::Tmhmm - Object for identifying transmembrane helixes in a given protein seequence.
# 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);
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)
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : program_name Usage : $factory>program_name() Function: holds the program name Returns: string Args : None
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 :
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
Title : new Usage : $rm->new(@params) Function: creates a new Tmhmm factory Returns: Bio::Tools::Run::Tmhmm Args :
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
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
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 :
Title : _run Usage : $obj->_run() Function: Internal(not to be used directly) Returns : An array of Bio::SeqFeature::Generic objects Args :
Title : _writeSeqFile Usage : obj->_writeSeqFile($seq) Function: Internal(not to be used directly) Returns : Args :