Langue: en

Version: 2005-04-27 (mandriva - 01/05/08)

Section: 3 (Bibliothèques de fonctions)


Bio::Tools::Run::Hmmer - Wrapper for local execution of hmmsearch ,hmmbuild, hmmcalibrate, hmmalign, hmmpfam


   #run hmmpfam|hmmalign|hmmsearch
   my $factory = Bio::Tools::Run::Hmmer->new('program'=>'hmmsearch','hmm'=>'model.hmm');
   # Pass the factory a Bio::Seq object or a file name
   # returns a Bio::SearchIO object
   my $search = $factory->run($seq);
   my @feat;
   while (my $result = $searchio->next_result){
    while(my $hit = $result->next_hit){
     while (my $hsp = $hit->next_hsp){
             print join("\t", ( $r->query_name,
                                )), "\n";
   #build a hmm using hmmbuild
   my $aio = Bio::AlignIO->new(-file=>"protein.msf",-format=>'msf');
   my $aln = $aio->next_aln;
   my $factory =  Bio::Tools::Run::Hmmer->new('program'=>'hmmbuild',
   #calibrate the hmm
   my $factory =  Bio::Tools::Run::Hmmer->new('program'=>'hmmcalibrate',
   my $factory =  Bio::Tools::Run::Hmmer->new('program'=>'hmmalign',
    # Pass the factory a Bio::Seq object or a file name
    # returns a Bio::AlignIO object
    my $aio = $factory->run($seq);


Wrapper module for Sean Eddy's HMMER suite of program to allow running of hmmsearch,hmmpfam,hmmalign, hmmbuild,hmmconvert. Binaries are available at


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AUTHOR - Shawn Hoon



  Shawn Hoon
  Jason Stajich jason -at- bioperl -dot- org
  Scott Markel scott -at- scitegic -dot com


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, obtiained from ENV variable.
  Returns:  string
  Args    :


  Title   : new
  Usage   : $HMMER->new(@params)
  Function: creates a new HMMER factory
  Returns:  Bio::Tools::Run::HMMER
  Args    :


  Title   :   run
  Usage   :   $obj->run($seqFile)
  Function:   Runs HMMER and returns Bio::SearchIO
  Returns :   A Bio::SearchIO
  Args    :   A Bio::PrimarySeqI or file name


  Title   :   _run
  Usage   :   $obj->_run()
  Function:   Internal(not to be used directly)
  Returns :   An array of Bio::SeqFeature::Generic objects
  Args    :


  Title   :  _setparams
  Usage   :  Internal function, not to be called directly
  Function:  creates a string of params to be used in the command string
  Example :
  Returns :  string of params
  Args    :


  Title   :   _writeSeqFile
  Usage   :   obj->_writeSeqFile($seq)
  Function:   Internal(not to be used directly)
  Returns :
  Args    :


  Title   :   _writeAlignFile
  Usage   :   obj->_writeAlignFile($seq)
  Function:   Internal(not to be used directly)
  Returns :
  Args    :