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Bio::Tools::Run::Tmhmm.3pm

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://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    :