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
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