NAME
Bio::Tools::Run::Hmmer - Wrapper for local execution of hmmalign, hmmbuild, hmmcalibrate, hmmemit, hmmpfam, hmmsearch
SYNOPSIS
my $factory = Bio::Tools::Run::Hmmer->new(-hmm => 'model.hmm');
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";
}
}
}
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);
$factory->calibrate();
my $seqio = $factory->hmmemit();
my $alnio = $factory->hmmalign(@seqs);
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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
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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:
AUTHOR - Shawn Hoon
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
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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
-_READMETHOD => 'hmmer' (default) || 'hmmer_pull'
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
-program => hmmalign|hmmbuild|hmmcalibrate|hmmemit|hmmpfam|hmmsearch
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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
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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
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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
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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
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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
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hmmpfam
Title : hmmpfam
Usage : $obj->hmmpfam()
Function: Runs hmmpfam
Returns : A Bio::SearchIO
Args : A Bio::PrimarySeqI, Bio::Align::AlignI or filename
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hmmsearch
Title : hmmsearch
Usage : $obj->hmmsearch()
Function: Runs hmmsearch
Returns : A Bio::SearchIO
Args : A Bio::PrimarySeqI, Bio::Align::AlignI or filename
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Title : _setinput
Usage : $obj->_setinput()
Function: Internal(not to be used directly)
Returns : filename
Args : A Bio::PrimarySeqI, Bio::Align::AlignI or filename
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_run
Title : _run
Usage : $obj->_run()
Function: Internal(not to be used directly)
Returns : Bio::SearchIO
Args : file name
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_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
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program_name
Title : program_name
Usage : $factory>program_name()
Function: holds the program name
Returns : string
Args : none
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program_dir
Title : program_dir
Usage : $factory->program_dir(@params)
Function: returns the program directory, obtained from ENV variable.
Returns : string
Args : none
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_writeSeqFile
Title : _writeSeqFile
Usage : obj->_writeSeqFile($seq)
Function: Internal(not to be used directly)
Returns : filename
Args : list of Bio::SeqI
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_writeAlignFile
Title : _writeAlignFile
Usage : obj->_writeAlignFile($seq)
Function: Internal(not to be used directly)
Returns : filename
Args : list of Bio::Align::AlignI
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