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.
[email protected] - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list: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 [email protected]
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