Bio::Tools::Run::Hmmer(3pm)				User Contributed Perl Documentation			       Bio::Tools::Run::Hmmer(3pm)

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("	", ( $result->query_name,
				      $hsp->query->start,
				      $hsp->query->end,
				      $hit->name,
				      $hsp->hit->start,
				      $hsp->hit->end,
				      $hsp->score,
				      $hsp->evalue,
				      $hsp->seq_str,
				      )), "
";
	   }
	  }
	 }

	 # 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

perl v5.12.3							    2011-06-18					       Bio::Tools::Run::Hmmer(3pm)