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

cpanm Bio::DB::ESoap

perl -MCPAN -e shell
install Bio::DB::ESoap