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