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)
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.
firstname.lastname@example.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:
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 :