NAME

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

SYNOPSIS

  # run hmmsearch (similar for hmmpfam)
  my $factory = Bio::Tools::Run::Hmmer->new(-hmm => 'model.hmm');

  # Pass the factory a Bio::Seq object or a file name, returns a Bio::SearchIO
  my $searchio = $factory->hmmsearch($seq);

  while (my $result = $searchio->next_result){
   while(my $hit = $result->next_hit){
    while (my $hsp = $hit->next_hsp){
            print join("\t", ( $result->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(-hmm => 'model.hmm');
  $factory->hmmbuild($aln);

  # calibrate the hmm
  $factory->calibrate();

  # emit a sequence stream from the hmm
  my $seqio = $factory->hmmemit();

  # align sequences to the hmm
  my $alnio = $factory->hmmalign(@seqs);

DESCRIPTION

Wrapper module for Sean Eddy's HMMER suite of program to allow running of hmmalign, hmmbuild, hmmcalibrate, hmmemit, hmmpfam and hmmsearch. Binaries are available at http://hmmer.janelia.org/

You can pass most options understood by the command-line programs to new(), or set the options by calling methods with the same name as the argument. In both instances, case sensitivity matters.

Additional methods are hmm() to specifiy the hmm file (needed for all HMMER programs) which you would normally set in the call to new().

The HMMER programs must either be in your path, or you must set the environment variable HMMERDIR to point to their location.

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

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

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 - 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
 Sendu Bala bix@sendu.me.uk

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

 Title   : new
 Usage   : $HMMER->new(@params)
 Function: Creates a new HMMER factory
 Returns : Bio::Tools::Run::HMMER
 Args    : -hmm => filename # the hmm, used by all program types; if not set
                            # here, must be set with hmm() method prior to
                            # running anything
           -_READMETHOD => 'hmmer' (default) || 'hmmer_pull' # the parsing
                                                             # module to use for
                                                             # hmmpfam/hmmsearch

           Any option supported by a Hmmer program, where switches are given
           a true value, eg. -q => 1, EXCEPT for the following which are handled
           internally/ incompatible: h verbose a compat pvm

           WARNING: the default sequence format passed to hmmpfam is msf. If
           you are using a different format, you need to pass it with informat.
           e.g.
           my $factory = Bio::Tools::Run::Hmmer->new(-hmm => 'model.hmm',
                                                     -informat => 'fasta');

           -q is synonymous with -quiet
           -o is synonymous with -outfile

           # may be specified here, allowing run() to be used, or
           # it can be omitted and the corresponding method (eg.
           # hmmalign()) used later.
           -program => hmmalign|hmmbuild|hmmcalibrate|hmmemit|hmmpfam|hmmsearch

run

 Title   : run
 Usage   : $obj->run($seqFile)
 Function: Runs one of the Hmmer programs, according to the current setting of
           program() (as typically set during new(-program => 'name')).
 Returns : A Bio::SearchIO, Bio::AlignIO, Bio::SeqIO or boolean depending on
           the program being run (see method corresponding to program name for
           details).
 Args    : A Bio::PrimarySeqI, Bio::Align::AlignI or filename

hmmalign

 Title   : hmmalign
 Usage   : $obj->hmmalign()
 Function: Runs hmmalign
 Returns : A Bio::AlignIO
 Args    : list of Bio::SeqI OR Bio::Align::AlignI OR filename of file with
           sequences or an alignment

hmmbuild

 Title   : hmmbuild
 Usage   : $obj->hmmbuild()
 Function: Runs hmmbuild, outputting an hmm to the file currently set by method
           hmm() or db(), or failing that, o() or outfile(), or failing that, to
           a temp location.
 Returns : true on success
 Args    : Bio::Align::AlignI OR filename of file with an alignment

hmmcalibrate

 Title   : hmmcalibrate
 Usage   : $obj->hmmcalibrate()
 Function: Runs hmmcalibrate
 Returns : true on success
 Args    : none (hmm() must be set, most likely by the -hmm option of new()), OR
           optionally supply an hmm filename to set hmm() and run

hmmemit

 Title   : hmmemit
 Usage   : $obj->hmmemit()
 Function: Runs hmmemit
 Returns : A Bio::SeqIO
 Args    : none (hmm() must be set, most likely by the -hmm option of new()), OR
           optionally supply an hmm filename to set hmm() and run

hmmpfam

 Title   : hmmpfam
 Usage   : $obj->hmmpfam()
 Function: Runs hmmpfam
 Returns : A Bio::SearchIO
 Args    : A Bio::PrimarySeqI, Bio::Align::AlignI or filename

hmmsearch

 Title   : hmmsearch
 Usage   : $obj->hmmsearch()
 Function: Runs hmmsearch
 Returns : A Bio::SearchIO
 Args    : A Bio::PrimarySeqI, Bio::Align::AlignI or filename

_setinput

 Title   : _setinput
 Usage   : $obj->_setinput()
 Function: Internal(not to be used directly)
 Returns : filename
 Args    : A Bio::PrimarySeqI, Bio::Align::AlignI or filename

_run

 Title   : _run
 Usage   : $obj->_run()
 Function: Internal(not to be used directly)
 Returns : Bio::SearchIO
 Args    : file name

_setparams

 Title   : _setparams
 Usage   : Internal function, not to be called directly
 Function: creates a string of params to be used in the command string
 Returns : string of params
 Args    : none

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.
 Returns : string
 Args    : none

_writeSeqFile

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

_writeAlignFile

 Title   : _writeAlignFile
 Usage   : obj->_writeAlignFile($seq)
 Function: Internal(not to be used directly)
 Returns : filename
 Args    : list of Bio::Align::AlignI