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.\" ========================================================================
.\"
.IX Title "Bio::Tools::Run::Hmmer 3pm"
.TH Bio::Tools::Run::Hmmer 3pm 2024-03-12 "perl v5.38.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH NAME
Bio::Tools::Run::Hmmer \- Wrapper for local execution of hmmalign, hmmbuild,
hmmcalibrate, hmmemit, hmmpfam, hmmsearch
.SH SYNOPSIS
.IX Header "SYNOPSIS"
.Vb 2
\&  # run hmmsearch (similar for hmmpfam)
\&  my $factory = Bio::Tools::Run::Hmmer\->new(\-hmm => \*(Aqmodel.hmm\*(Aq);
\&
\&  # 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("\et", ( $result\->query_name,
\&                               $hsp\->query\->start,
\&                               $hsp\->query\->end,
\&                               $hit\->name,
\&                               $hsp\->hit\->start,
\&                               $hsp\->hit\->end,
\&                               $hsp\->score,
\&                               $hsp\->evalue,
\&                               $hsp\->seq_str,
\&                               )), "\en";
\&    }
\&   }
\&  }
\&
\&  # build a hmm using hmmbuild
\&  my $aio = Bio::AlignIO\->new(\-file => "protein.msf", \-format => \*(Aqmsf\*(Aq);
\&  my $aln = $aio\->next_aln;
\&  my $factory =  Bio::Tools::Run::Hmmer\->new(\-hmm => \*(Aqmodel.hmm\*(Aq);
\&  $factory\->hmmbuild($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);
.Ve
.SH DESCRIPTION
.IX Header "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/
.PP
You can pass most options understood by the command-line programs to \fBnew()\fR, or
set the options by calling methods with the same name as the argument. In both
instances, case sensitivity matters.
.PP
Additional methods are \fBhmm()\fR to specifiy the hmm file (needed for all HMMER
programs) which you would normally set in the call to \fBnew()\fR.
.PP
The HMMER programs must either be in your path, or you must set the environment
variable HMMERDIR to point to their location.
.SH FEEDBACK
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS Support
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  http://redmine.open\-bio.org/projects/bioperl/
.Ve
.SH "AUTHOR \- Shawn Hoon"
.IX Header "AUTHOR - Shawn Hoon"
.Vb 1
\& Email: shawnh\-at\-gmx.net
.Ve
.SH CONTRIBUTORS
.IX Header "CONTRIBUTORS"
.Vb 4
\& 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
.Ve
.SH APPENDIX
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
.SS new
.IX Subsection "new"
.Vb 10
\& 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 => \*(Aqhmmer\*(Aq (default) || \*(Aqhmmer_pull\*(Aq # 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 => \*(Aqmodel.hmm\*(Aq,
\&                                                     \-informat => \*(Aqfasta\*(Aq);
\&
\&           \-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
.Ve
.SS run
.IX Subsection "run"
.Vb 8
\& 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 => \*(Aqname\*(Aq)).
\& 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
.Ve
.SS hmmalign
.IX Subsection "hmmalign"
.Vb 6
\& 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
.Ve
.SS hmmbuild
.IX Subsection "hmmbuild"
.Vb 7
\& 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
.Ve
.SS hmmcalibrate
.IX Subsection "hmmcalibrate"
.Vb 6
\& 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
.Ve
.SS hmmemit
.IX Subsection "hmmemit"
.Vb 6
\& 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
.Ve
.SS hmmpfam
.IX Subsection "hmmpfam"
.Vb 5
\& Title   : hmmpfam
\& Usage   : $obj\->hmmpfam()
\& Function: Runs hmmpfam
\& Returns : A Bio::SearchIO
\& Args    : A Bio::PrimarySeqI, Bio::Align::AlignI or filename
.Ve
.SS hmmsearch
.IX Subsection "hmmsearch"
.Vb 5
\& Title   : hmmsearch
\& Usage   : $obj\->hmmsearch()
\& Function: Runs hmmsearch
\& Returns : A Bio::SearchIO
\& Args    : A Bio::PrimarySeqI, Bio::Align::AlignI or filename
.Ve
.SS _setinput
.IX Subsection "_setinput"
.Vb 5
\& Title   : _setinput
\& Usage   : $obj\->_setinput()
\& Function: Internal(not to be used directly)
\& Returns : filename
\& Args    : A Bio::PrimarySeqI, Bio::Align::AlignI or filename
.Ve
.SS _run
.IX Subsection "_run"
.Vb 5
\& Title   : _run
\& Usage   : $obj\->_run()
\& Function: Internal(not to be used directly)
\& Returns : Bio::SearchIO
\& Args    : file name
.Ve
.SS _setparams
.IX Subsection "_setparams"
.Vb 5
\& 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
.Ve
.SS program_name
.IX Subsection "program_name"
.Vb 5
\& Title   : program_name
\& Usage   : $factory>program_name()
\& Function: holds the program name
\& Returns : string
\& Args    : none
.Ve
.SS program_dir
.IX Subsection "program_dir"
.Vb 5
\& Title   : program_dir
\& Usage   : $factory\->program_dir(@params)
\& Function: returns the program directory, obtained from ENV variable.
\& Returns : string
\& Args    : none
.Ve
.SS _writeSeqFile
.IX Subsection "_writeSeqFile"
.Vb 5
\& Title   : _writeSeqFile
\& Usage   : obj\->_writeSeqFile($seq)
\& Function: Internal(not to be used directly)
\& Returns : filename
\& Args    : list of Bio::SeqI
.Ve
.SS _writeAlignFile
.IX Subsection "_writeAlignFile"
.Vb 5
\& Title   : _writeAlignFile
\& Usage   : obj\->_writeAlignFile($seq)
\& Function: Internal(not to be used directly)
\& Returns : filename
\& Args    : list of Bio::Align::AlignI
.Ve