NAME

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

SYNOPSIS

  #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,
                               $hsp->query->start,
                               $hsp->query->end,
                               $hit->name,
                               $hsp->hit->start,
                               $hsp->hit->end,
                               $hsp->score,
                               $hsp->evalue,
                               $hsp->seq_str,
                               )), "\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',
                                             'hmm'=>'model.hmm');
  $factory->run($aln);

  #calibrate the hmm
  my $factory =  Bio::Tools::Run::Hmmer->new('program'=>'hmmcalibrate',
                                             'hmm'=>'model.hmm');
  $factory->run();

  my $factory =  Bio::Tools::Run::Hmmer->new('program'=>'hmmalign',
                                             'hmm'=>'model.hmm');

   # Pass the factory a Bio::Seq object or a file name

   # returns a Bio::AlignIO object
   my $aio = $factory->run($seq);

DESCRIPTION

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

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

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 - Shawn Hoon

 Email: shawnh-at-gmx.net

CONTRIBUTORS

 Shawn Hoon shawnh-at-gmx.net
 Jason Stajich jason -at- bioperl -dot- org
 Scott Markel scott -at- scitegic -dot com

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, obtiained from ENV variable.
 Returns:  string
 Args    :

new

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

run

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

_run

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

_setparams

 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    :  

_writeSeqFile

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

_writeAlignFile

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

cpanm Bio::Factory::EMBOSS

perl -MCPAN -e shell
install Bio::Factory::EMBOSS