Christopher Fields > BioPerl-Run > Bio::Tools::Run::Tmhmm

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BioPerl-Run-1.006900.tar.gz

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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    :
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