# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Tools::Run::Hmmer - Wrapper for local execution of hmmalign, hmmbuild,
hmmcalibrate, hmmemit, hmmpfam, hmmsearch
=head1 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);
=head1 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.
=head1 FEEDBACK
=head2 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
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=head2 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/
=head1 AUTHOR - Shawn Hoon
Email: shawnh-at-gmx.net
=head1 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
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
package Bio::Tools::Run::Hmmer;
use strict;
use Bio::SeqIO;
use Bio::SearchIO;
use Bio::AlignIO;
use base qw(Bio::Tools::Run::WrapperBase);
our $DefaultFormat = 'msf';
our $DefaultReadMethod = 'hmmer';
our %ALL = (quiet => 'q', o => 'outfile');
our @ALIGN_PARAMS = qw(mapali outformat withali o);
our @ALIGN_SWITCHES = qw(m oneline q);
our @BUILD_PARAMS = qw(n archpri cfile gapmax idlevel null pam pamwgt
pbswitch prior swentry swexit o);
our @BUILD_SWITCHES = qw(f g s A F amino binary fast hand noeff nucleic
wblosum wgsc wme wnone wpb wvoronoi);
our @CALIBRATE_PARAMS = qw(fixed histfile mean num sd seed cpu);
our @CALIBRATE_SWITCHES = qw();
our @EMIT_PARAMS = qw(n seed o);
our @EMIT_SWITCHES = qw(c q);
our @PFAM_PARAMS = qw(A E T Z domE domT informat cpu);
our @PFAM_SWITCHES = qw(n acc cut_ga cut_gc cut_nc forward null2 xnu);
our @SEARCH_PARAMS = @PFAM_PARAMS;
our @SEARCH_SWITCHES = @PFAM_SWITCHES;
our %OTHER = (_READMETHOD => '_readmethod',
program_name => [qw(PROGRAM program)],
hmm => [qw(HMM db DB)]);
# just to be explicit
our @UNSUPPORTED = qw(h verbose a compat pvm);
=head2 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 $factory = Bio::Tools::Run::Hmmer->new(-hmm => 'model.hmm',
-informat => 'fasta');
-q is synonymous with -quiet
-o is synonymous with -outfile
# may be specified here, allowing run() to be used, or
# it can be omitted and the corresponding method (eg.
# hmmalign()) used later.
-program => hmmalign|hmmbuild|hmmcalibrate|hmmemit|hmmpfam|hmmsearch
=cut
sub new {
my($class, @args) = @_;
my $self = $class->SUPER::new(@args);
$self->_set_from_args(\@args, -methods => {(map { $_ => $ALL{$_} } keys %ALL),
(map { $_ => $OTHER{$_} } keys %OTHER),
(map { $_ => $_ }
(@ALIGN_PARAMS,
@ALIGN_SWITCHES,
@BUILD_PARAMS,
@BUILD_SWITCHES,
@CALIBRATE_PARAMS,
@CALIBRATE_SWITCHES,
@EMIT_PARAMS,
@EMIT_SWITCHES,
@PFAM_PARAMS,
@PFAM_SWITCHES,
@SEARCH_PARAMS,
@SEARCH_SWITCHES))},
-create => 1,
-case_sensitive => 1);
$self->informat || $self->informat($DefaultFormat);
$self->_READMETHOD || $self->_READMETHOD($DefaultReadMethod);
return $self;
}
=head2 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
=cut
sub run {
my $self = shift;
my $program = lc($self->program_name || $self->throw("The program must already be specified"));
$self->can($program) || $self->throw("'$program' wasn't a valid program");
return $self->$program(@_);
}
=head2 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
=cut
sub hmmalign {
my $self = shift;
$self->program_name('hmmalign');
my $input = $self->_setinput(@_);
unless (defined $self->o()) {
$self->q(1);
}
if (! $self->outformat) {
$self->outformat($DefaultFormat);
}
return $self->_run($input);
}
=head2 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
=cut
sub hmmbuild {
my $self = shift;
$self->program_name('hmmbuild');
my $input = $self->_setinput(@_);
unless (defined $self->hmm()) {
$self->hmm($self->o() || $self->io->tempfile(-dir => $self->tempdir));
}
return $self->_run($input);
}
=head2 hmmcalibrate
Title : hmmcalibrate
Usage : $obj->hmmcalibrate()
Function: Runs hmmcalibrate
Returns : true on success
Args : none (hmm() must be set, most likely by the -hmm option of new()), OR
optionally supply an hmm filename to set hmm() and run
=cut
sub hmmcalibrate {
my ($self, $hmm) = @_;
$self->program_name('hmmcalibrate');
$self->hmm($hmm) if $hmm;
$self->hmm || $self->throw("hmm() must be set first");
return $self->_run();
}
=head2 hmmemit
Title : hmmemit
Usage : $obj->hmmemit()
Function: Runs hmmemit
Returns : A Bio::SeqIO
Args : none (hmm() must be set, most likely by the -hmm option of new()), OR
optionally supply an hmm filename to set hmm() and run
=cut
sub hmmemit {
my ($self, $hmm) = @_;
$self->program_name('hmmemit');
$self->hmm($hmm) if $hmm;
$self->hmm || $self->throw("hmm() must be set first");
unless (defined $self->o()) {
$self->q(1);
}
return $self->_run();
}
=head2 hmmpfam
Title : hmmpfam
Usage : $obj->hmmpfam()
Function: Runs hmmpfam
Returns : A Bio::SearchIO
Args : A Bio::PrimarySeqI, Bio::Align::AlignI or filename
=cut
sub hmmpfam {
my $self = shift;
$self->program_name('hmmpfam');
my $input = $self->_setinput(@_);
return $self->_run($input);
}
=head2 hmmsearch
Title : hmmsearch
Usage : $obj->hmmsearch()
Function: Runs hmmsearch
Returns : A Bio::SearchIO
Args : A Bio::PrimarySeqI, Bio::Align::AlignI or filename
=cut
sub hmmsearch {
my $self = shift;
$self->program_name('hmmsearch');
my $input = $self->_setinput(@_);
return $self->_run($input);
}
=head2 _setinput
Title : _setinput
Usage : $obj->_setinput()
Function: Internal(not to be used directly)
Returns : filename
Args : A Bio::PrimarySeqI, Bio::Align::AlignI or filename
=cut
sub _setinput {
my ($self, @things) = @_;
@things || $self->throw("At least one input is required");
my $infile;
if (ref $things[0] && $things[0]->isa("Bio::PrimarySeqI") ){# it is an object
$infile = $self->_writeSeqFile(@things);
}
elsif(ref $things[0] && $things[0]->isa("Bio::Align::AlignI")){
$infile = $self->_writeAlignFile(@things);
}
elsif (-e $things[0]) {
$infile = $things[0];
}
else {
$self->throw("Unknown kind of input '@things'");
}
return $infile;
}
=head2 _run
Title : _run
Usage : $obj->_run()
Function: Internal(not to be used directly)
Returns : Bio::SearchIO
Args : file name
=cut
sub _run {
my ($self, $file) = @_;
# Use double quotes if file path have empty spaces
if ($file =~ m/ /) {
$file = "\"$file\"";
}
my $str = $self->executable;
# Use double quotes if executable path have empty spaces
if ($str =~ m/ /) {
$str = "\"$str\"";
}
$str .= $self->_setparams;
$str .= ' '.$file if $file;
$self->debug("HMMER command = $str");
my $progname = $self->program_name;
my @in;
my @verbose = (-verbose => $self->verbose);
if ($progname =~ /align|build|emit/) {
my $outfile = $self->o;
if ($outfile || $progname eq 'hmmbuild') {
my $null = ($^O =~ m/mswin/i) ? 'NUL' : '/dev/null';
$str .= " > $null" if $self->quiet;
if ($progname eq 'hmmbuild') {
my $status = system($str);
return $status ? 0 : 1;
}
else {
system($str) && $self->throw("HMMER call ($str) crashed: $?\n");
@in = (-file => $outfile);
}
}
else {
open(my $fh, "$str |") || $self->throw("HMMER call ($str) crashed: $?\n");
@in = (-fh => $fh);
}
}
elsif ($progname =~ /pfam|search/i) {
open(my $fh, "$str |") || $self->throw("HMMER call ($str) crashed: $?\n");
return Bio::SearchIO->new(-fh => $fh,
@verbose,
-format => $self->_READMETHOD);
}
if ($progname eq 'hmmalign') {
return Bio::AlignIO->new(@in,
@verbose,
-format => $self->outformat);
}
elsif ($progname eq 'hmmemit') {
return Bio::SeqIO->new(@in,
@verbose,
-format => 'fasta');
}
elsif ($progname =~ /calibrate/) {
my $null = ($^O =~ m/mswin/i) ? 'NUL' : '/dev/null';
$str .= " > $null 2> $null" if $self->quiet;
my $status = system($str);
return $status ? 0 : 1;
}
}
=head2 _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
=cut
sub _setparams {
my $self = shift;
my @execparams;
my @execswitches;
SWITCH: for ($self->program_name) {
/align/ && do { @execparams = @ALIGN_PARAMS;
@execswitches = @ALIGN_SWITCHES;
last SWITCH; };
/build/ && do { @execparams = @BUILD_PARAMS;
@execswitches = @BUILD_SWITCHES;
last SWITCH; };
/calibrate/ && do { @execparams = @CALIBRATE_PARAMS;
@execswitches = @CALIBRATE_SWITCHES;
last SWITCH; };
/emit/ && do { @execparams = @EMIT_PARAMS;
@execswitches = @EMIT_SWITCHES;
last SWITCH; };
/pfam/ && do { @execparams = @PFAM_PARAMS;
@execswitches = @PFAM_SWITCHES;
last SWITCH; };
/search/ && do { @execparams = @SEARCH_PARAMS;
@execswitches = @SEARCH_SWITCHES;
last SWITCH; };
}
my $param_string = $self->SUPER::_setparams(-params => \@execparams,
-switches => \@execswitches,
-mixed_dash => 1);
my $hmm = $self->hmm || $self->throw("Need to specify either HMM file or Database");
# Use double quotes if hmm path have empty spaces
if ($hmm =~ m/ /) {
$hmm = "\"$hmm\"";
}
$param_string .= ' '.$hmm;
return $param_string;
}
=head2 program_name
Title : program_name
Usage : $factory>program_name()
Function: holds the program name
Returns : string
Args : none
=cut
sub program_name {
my $self = shift;
if (@_) {
$self->{program_name} = shift;
# hack so that when program_name changes, so does executable()
delete $self->{'_pathtoexe'};
}
return $self->{program_name} || '';
}
=head2 program_dir
Title : program_dir
Usage : $factory->program_dir(@params)
Function: returns the program directory, obtained from ENV variable.
Returns : string
Args : none
=cut
sub program_dir {
return $ENV{HMMERDIR} if $ENV{HMMERDIR};
}
=head2 _writeSeqFile
Title : _writeSeqFile
Usage : obj->_writeSeqFile($seq)
Function: Internal(not to be used directly)
Returns : filename
Args : list of Bio::SeqI
=cut
sub _writeSeqFile {
my ($self, @seq) = @_;
my ($tfh, $inputfile) = $self->io->tempfile(-dir=>$self->tempdir);
$self->informat('fasta');
my $out = Bio::SeqIO->new(-fh => $tfh , '-format' => 'fasta');
foreach my $s (@seq) {
$out->write_seq($s);
}
$out->close();
$out = undef;
close($tfh);
undef $tfh;
return $inputfile;
}
=head2 _writeAlignFile
Title : _writeAlignFile
Usage : obj->_writeAlignFile($seq)
Function: Internal(not to be used directly)
Returns : filename
Args : list of Bio::Align::AlignI
=cut
sub _writeAlignFile{
my ($self, @align) = @_;
my ($tfh, $inputfile) = $self->io->tempfile(-dir=>$self->tempdir);
my $out = Bio::AlignIO->new('-fh' => $tfh, '-format' => $self->informat);
foreach my $a (@align) {
$out->write_aln($a);
}
$out->close();
$out = undef;
close($tfh);
undef $tfh;
return $inputfile;
}
1;