#
# BioPerl module for Bio::Tools::Run::RNAMotif
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Chris Fields
#
# Copyright Chris Fields
#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
=head1 NAME
Bio::Tools::Run::RNAMotif - Wrapper for local execution of rnamotif, rm2ct,
rmfmt, rmprune
=head1 SYNOPSIS
#run rnamotif|rmfmt|rm2ct
my @params = (
descr => 'pyrR.descr',
fmt => 'gb',
setvar => 'ctx_maxlen=20',
context => 1,
sh => 1,
);
my $factory = Bio::Tools::Run::RNAMotif->new(-program =>'rnamotif',
-prune => 1,
@params);
# Pass the factory a Bio::Seq object or a file name
# Returns a Bio::SearchIO object
#my $searchio = $factory->run("B_sub.gb");
my $searchio = $factory->run($seq);
while (my $result = $searchio->next_result){
while(my $hit = $result->next_hit){
while (my $hsp = $hit->next_hsp){
print join("\t", ( $r->query_name,
$hit->name,
$hsp->hit->start,
$hsp->hit->end,
$hsp->meta,
$hsp->score,
)), "\n";
}
}
}
# Pass a finished report through rmfmt (-a format only)
# Returns Bio::AlignIO object
my $aio = Bio::AlignIO->new(-file=>"rna.msf",-format=>'msf');
my $factory = Bio::Tools::Run::RNAMotif->new('program'=>'rmfmt',
'a' => 1);
my $alnin = $factory->run('trna.rnamotif');
my $aln = $alnin->next_aln;
$aio->write_aln($aln);
=head1 DESCRIPTION
Wrapper module for Tom Macke and David Cases's RNAMotif suite of programs. This
allows running of rnamotif, rmprune, rm2ct, and rmfmt. Binaries are available at
http://www.scripps.edu/mb/case/casegr-sh-3.5.html.
This wrapper allows for one to save output to an optional named file or tempfile
using the '-outfile_name' or '-tempfile' parameters; this is primarily for
saving output from the rm2ct program, which currently does not have a parser
available. If both a named output file and tempfile flag are set, the output
file name is used. The default setting is piping output into a filehandle for
parsing (or output to STDERR, for rm2ct which requires '-verbose' set to 1).
WARNING: At this time, there is very little checking of parameter settings, so
one could have an error if setting the worng parameter for a program. Future
versions will likely add some error checking.
=head1 NOTES ON PROGRAM PARAMETERS
All program parameters are currently supported. Of note, the 'D' parameter, used
for setting the value of a variable to a value, is changed to 'set_var' to avoid
name collisions with 'd' (used for dumping internal data structures).
=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 - Chris Fields
Email: cjfields-at-uiuc-dot-edu
=head1 CONTRIBUTORS
cjfields-at-uiuc-dot-edu
=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::RNAMotif;
use strict;
use Bio::SeqIO;
use Bio::Root::Root;
use Bio::SearchIO;
use Bio::AlignIO;
use Bio::Tools::Run::WrapperBase;
use base qw(Bio::Root::Root Bio::Tools::Run::WrapperBase);
# will move parameters to each program, use this for _set_params
my %RNAMOTIF_PROGS =(
rnamotif => [qw(c d h N O p s v context sh setvar I xdfname pre post
descr xdescr fmt fmap )],
rm2ct => [qw(t)],
rmfmt => [qw(a l la smax td)],
rmprune => [] # no params
);
my %RNAMOTIF_SWITCHES = map {$_ => 1} qw(c d h p s v l a la context sh);
# order is important here
my @RNAMOTIF_PARAMS=qw(program prune c sh N d h p s v context setvar O I
xdfname pre post descr xdescr fmt fmap l a la t);
=head2 new
Title : new
Usage : my $wrapper = Bio::Tools::Run::RNAMotif->new(@params)
Function: creates a new RNAMotif factory
Returns: Bio::Tools::Run::RNAMotif
Args : list of parameters
-tempfile => set tempfile flag (default 0)
-outfile_name => set file to send output to (default none)
-prune => set rmprune postprocess flag (default 0)
=cut
sub new {
my ($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($out, $tf) = $self->_rearrange([qw(OUTFILE_NAME TEMPFILE)], @args);
$self->io->_initialize_io();
if ($tf && !$out) {
my ($tfh, $outfile) = $self->io->tempfile(-dir=>$self->tempdir());
close($tfh);
undef $tfh;
$self->outfile_name($outfile);
} else {
$out ||= '';
$self->outfile_name($out);
}
$tf && $self->tempfile($tf);
$self->_set_from_args(\@args,
-methods => [@RNAMOTIF_PARAMS],
-create => 1
);
return $self;
}
=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;
return $self->program(@_);
}
=head2 program_dir
Title : program_dir
Usage : $factory->program_dir(@params)
Function: returns the program directory, obtained from ENV variable.
Returns: string
Args :
=cut
sub program_dir {
return Bio::Root::IO->catfile($ENV{RNAMOTIFDIR}) if $ENV{RNAMOTIFDIR};
}
=head2 version
Title : version
Usage : $v = $prog->version();
Function: Determine the version number of the program
Example :
Returns : float or undef
Args : none
=cut
sub version {
my ($self) = @_;
return undef unless $self->executable;
return $self->{'_progversion'} if $self->{'_progversion'};
my $string = `rnamotif -v 2>&1`;
my $v;
if ($string =~ m{([\d.]+)}) {
$v = $1;
}
return $self->{'_progversion'} = $v || $string;
}
=head2 run
Title : run
Usage : $obj->run($seqFile)
Function: Runs RNAMotif programs, returns Bio::SearchIO/Bio::AlignIO
Returns : Depends on program:
'rnamotif' - returns Bio::SearchIO
'rmfmt -a' - returns Bio::AlignIO
all others - sends output to outfile, tempfile, STDERR
Use search() (for Bio::SearchIO stream) or get_AlignIO() (for
Bio::AlignIO stream) for a uniform Bioperl object interface.
Args : A Bio::PrimarySeqI or file name
Note : This runs any RNAMotif program set via program()
=cut
sub run {
my ($self,@seq) = @_;
$self->throw ("Must pass a file name or a list of Bio::PrimarySeqI objects")
if (!@seq);
if (ref $seq[0] && $seq[0]->isa("Bio::PrimarySeqI") ){# it is an object
my $infile1 = $self->_writeSeqFile(@seq);
return $self->_run($infile1);
} else {
return $self->_run(@seq);
}
}
=head2 search
Title : search
Usage : $searchio = $obj->search($seqFile)
Function: Runs 'rnamotif' on seqs, returns Bio::SearchIO
Returns : A Bio::SearchIO
Args : A Bio::PrimarySeqI or file name
Note : Runs 'rnamotif' only, regardless of program setting; all other
parameters loaded
=cut
sub search {
my ($self,@seq) = @_;
$self->throw ("Must pass a file name or a list of Bio::PrimarySeqI objects")
if (!@seq);
if (ref $seq[0] && $seq[0]->isa("Bio::PrimarySeqI") ){# it is an object
my $infile1 = $self->_writeSeqFile(@seq);
return $self->_run($infile1);
} else {
return $self->_run(@seq);
}
}
=head2 get_AlignIO
Title : get_AlignIO
Usage : $aln = $obj->get_AlignIO($seqFile)
Function: Runs 'rmfmt -a' on file, returns Bio::AlignIO
Returns : A Bio::AlignIO
Args : File name
Note : Runs 'rmfmt -a' only, regardless of program setting; only file
name and outfile (if any) are set
=cut
sub get_AlignIO {
my ($self,@seq) = @_;
$self->throw ("Must pass a file name")
if (!@seq && ref($seq[0]));
return $self->_run(@seq);
}
=head2 tempfile
Title : tempfile
Usage : $obj->tempfile(1)
Function: Set tempfile flag. When set, writes output to a tempfile; this
is overridden by outfile_name() if set
Returns : Boolean setting (or undef if not set)
Args : [OPTIONAL] Boolean
=cut
sub tempfile {
my $self = shift;
return $self->{'_tempfile'} = shift if @_;
return $self->{'_tempfile'};
}
=head2 prune
Title : prune
Usage : $obj->prune(1)
Function: Set rmprune flag. When set, follows any searches with a call to
rmprune (this deletes some redundant sequence hits)
Returns : Boolean setting (or undef if not set)
Args : [OPTIONAL] Boolean
=cut
sub prune {
my $self = shift;
return $self->{'_prune'} = shift if @_;
return $self->{'_prune'};
}
=head2 _run
Title : _run
Usage : $obj->_run()
Function: Internal(not to be used directly)
Returns :
Args :
=cut
sub _run {
my ($self,$file,$prog)= @_;
return unless $self->executable;
$self->io->_io_cleanup();
my ($str, $progname, $outfile) =
($prog || $self->executable, $self->program_name, $self->outfile_name);
my $param_str = $self->_setparams($file);
my $descr = ($self->can('descr')) ? $self->descr :
($self->can('xdescr')) ? $self->xdescr :
$self->throw("Must have a descriptor present!");
$str .= " $param_str";
$self->debug("RNAMotif command: $str\n");
# rnamotif => SearchIO object
# rmfmt -a => AlignIO object
# all others sent to outfile, tempfile, or STDERR (upon verbose = 1)
my $obj = ($progname eq 'rnamotif' || $progname eq 'rmprune' ) ?
Bio::SearchIO->new(-verbose => $self->verbose,
-format => "rnamotif",
-version => $self->version,
-database => $file,
-model => $descr) :
($progname eq 'rmfmt' && $self->can('a') && $self->a) ?
Bio::AlignIO->new(-verbose => $self->verbose, -format =>'fasta') :
undef;
my @args;
# file-based
if ($outfile) {
local $SIG{CHLD} = 'DEFAULT';
my $status = system($str);
if($status || !-e $outfile ) {
my $error = ($!) ? "$! Status: $status" : "Status: $status";
$self->throw( "RNAMotif call crashed: $error \n[command $str]\n");
return undef;
}
if ($obj && ref($obj)) {
$obj->file($outfile);
@args = (-file => $outfile);
}
# fh-based
} else {
open(my $fh,"$str |") || $self->throw("RNAMotif call ($str) crashed: $?\n");
if ($obj && ref($obj)) {
$obj->fh($fh);
@args = (-fh => $fh);
} else {
# dump to debugging
my $io;
while(<$fh>) {$io .= $_;}
close($fh);
$self->debug($io);
return 1;
}
}
# initialize SearchIO/AlignIO...um...IO
# (since file/fh set post obj construction)
$obj->_initialize_io(@args) if $obj && ref($obj);
return $obj || 1;
}
=head2 _setparams
Title : _setparams
Usage : Internal function, not to be called directly
Function: creates a string of params to be used in the command string
Example :
Returns : string of params
Args :
=cut
sub _setparams {
my ($self, $file) = @_;
my $progname = $self->program_name;
# small sanity check
$self->throw("Unknown program: $progname") if
(!exists $RNAMOTIF_PROGS{$progname} );
my $param_string;
my $outfile = ($self->outfile_name) ? ' > '.$self->outfile_name : '';
my @params;
foreach my $attr (@RNAMOTIF_PARAMS) {
next if ($attr =~/PROGRAM|DB|PRUNE/i);
my $value = $self->$attr();
next unless (defined $value);
my $attr_key = '-'.$attr;
if (exists $RNAMOTIF_SWITCHES{$attr}) {
push @params, $attr_key;
} else {
if ($attr eq 'setvar') {
push @params, '-D'.$value;
} else {
push @params, $attr_key.' '.$value;
}
}
}
$param_string = join ' ', @params;
$param_string .= ' '.$file;
if ($self->prune && $self->program_name eq 'rnamotif') {
$param_string .= ' | rmprune';
}
$param_string .= $outfile;
return $param_string;
}
=head2 _writeSeqFile
Title : _writeSeqFile
Usage : obj->_writeSeqFile($seq)
Function: Internal(not to be used directly)
Returns : writes passed Seq objects to tempfile, to be used as input
for program
Args :
=cut
sub _writeSeqFile {
my ($self,@seq) = @_;
my ($tfh,$inputfile) = $self->io->tempfile(-dir=>$self->tempdir);
my $in = Bio::SeqIO->new(-fh => $tfh , '-format' => 'fasta');
foreach my $s(@seq){
$in->write_seq($s);
}
$in->close();
$in = undef;
close($tfh);
undef $tfh;
return $inputfile;
}
1;