# BioPerl module for RepeatMasker
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Shawn Hoon <shawnh@fugu-sg.org>
#
# Copyright Shawn Hoon
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Tools::Run::RepeatMasker - Wrapper for RepeatMasker Program
=head1 SYNOPSIS
use Bio::Tools::Run::RepeatMasker;
my @params=("mam" => 1,"noint"=>1);
my $factory = Bio::Tools::Run::RepeatMasker->new(@params);
$in = Bio::SeqIO->new(-file => "contig1.fa",
-format => 'fasta');
my $seq = $in->next_seq();
#return an array of Bio::SeqFeature::FeaturePair objects
my @feats = $factory->run($seq);
# or
$factory->run($seq);
my @feats = $factory->repeat_features;
#return the masked sequence, a Bio::SeqI object
my $masked_seq = $factory->run;
=head1 DESCRIPTION
To use this module, the RepeatMasker program (and probably database) must be
installed. RepeatMasker is a program that screens DNA sequences for interspersed
repeats known to exist in mammalian genomes as well as for low
complexity DNA sequences. For more information, on the program and its
usage, please refer to http://www.repeatmasker.org/.
Having installed RepeatMasker, you must let Bioperl know where it is.
This can be done in (at least) three ways:
1. Make sure the RepeatMasker executable is in your path.
2. Define an environmental variable REPEATMASKERDIR which is a
directory which contains the RepeatMasker executable:
In bash:
export REPEATMASKERDIR=/home/username/RepeatMasker/
In csh/tcsh:
setenv REPEATMASKERDIR /home/username/RepeatMasker/
3. Include a definition of an environmental variable REPEATMASKERDIR in
every script that will use this RepeatMasker wrapper module, e.g.:
BEGIN { $ENV{REPEATMASKERDIR} = '/home/username/RepeatMasker/' }
use Bio::Tools::Run::RepeatMasker;
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:
http://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Shawn Hoon
Email shawnh@fugu-sg.org
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a "_".
=cut
package Bio::Tools::Run::RepeatMasker;
use vars qw($AUTOLOAD @ISA $PROGRAM $PROGRAMDIR $PROGRAMNAME
@RM_SWITCHES @RM_PARAMS @OTHER_SWITCHES %OK_FIELD);
use strict;
use Bio::SeqFeature::Generic;
use Bio::SeqFeature::FeaturePair;
use Bio::Root::Root;
use Bio::Tools::Run::WrapperBase;
use Bio::Tools::RepeatMasker;
# Let the code begin...
@ISA = qw(Bio::Root::Root Bio::Tools::Run::WrapperBase );
BEGIN {
@RM_PARAMS = qw(DIR DIV LIB CUTOFF PARALLEL GC FRAG SPECIES MAXSIZE );
@RM_SWITCHES = qw(NOLOW LOW L NOINT INT NORNA ALU M MUS ROD
RODENT MAM MAMMAL COW AR
ARABIDOPSIS DR DROSOPHILA EL ELEGANS
IS_ONLY IS_CLIP NO_IS RODSPEC E EXCLN
NO_ID FIXED XM U GFF ACE POLY X XSMALL SMALL
INV A ALIGNMENTS
PRIMSPEC W WUBLAST S Q QQ GCCALC NOCUT);
@OTHER_SWITCHES = qw(NOISY QUIET SILENT);
# Authorize attribute fields
foreach my $attr ( @RM_PARAMS, @RM_SWITCHES,
@OTHER_SWITCHES) { $OK_FIELD{$attr}++; }
}
=head2 program_name
Title : program_name
Usage : $factory>program_name()
Function: holds the program name
Returns: string
Args : None
=cut
sub program_name {
return 'RepeatMasker';
}
=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{REPEATMASKERDIR}) if $ENV{REPEATMASKERDIR};
}
sub AUTOLOAD {
my $self = shift;
my $attr = $AUTOLOAD;
$attr =~ s/.*:://;
$attr = uc $attr;
$self->throw("Unallowed parameter: $attr !") unless $OK_FIELD{$attr};
$self->{$attr} = shift if @_;
return $self->{$attr};
}
=head2 new
Title : new
Usage : $rm->new($seq)
Function: creates a new wrapper
Returns: Bio::Tools::Run::RepeatMasker
Args : self
=cut
sub new {
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
my ($attr, $value);
# Need to check that filehandle is not left open here...
while (@args) {
$attr = shift @args;
$value = shift @args;
next if( $attr =~ /^-/ ); # don't want named parameters
$self->$attr($value);
}
# unless ($self->executable()) {
# if( $self->verbose >= 0 ) {
# warn "RepeatMasker program not found as ".($self->executable||'').
# " or not executable. \n";
# }
# }
return $self;
}
=head2 version
Title : version
Usage :
Function: Determine the version number of the program
Example :
Returns : float or undef
Args : none
=cut
sub version {
my ($self) = @_;
return $self->{'_version'} if( defined $self->{'_version'} );
my $exe = $self->executable;
return undef unless $exe;
my $string = `$exe -- ` ;
if( $string =~ /\(([\d.]+)\)/ ||
$string =~ /RepeatMasker\s+version\s+(\S+)/ ) {
return $self->{'_version'} = $1;
} else {
return $self->{'_version'} = undef;
}
}
=head2 run
Title : run
Usage : $rm->run($seq);
Function: Run Repeatmasker on the sequence set as
the argument
Returns : an array of repeat features that are
Bio::SeqFeature::FeaturePairs
Args : Bio::PrimarySeqI compliant object
=cut
sub run {
my ($self,$seq) = @_;
my ($infile);
$infile = $self->_setinput($seq);
my $param_string = $self->_setparams();
my @repeat_feats = $self->_run($infile,$param_string);
return @repeat_feats;
}
=head2 mask
Title : mask
Usage : $rm->mask($seq)
Function: This method is deprecated. Call run() instead
Example :
Returns : an array of repeat features that are
Bio::SeqFeature::FeaturePairs
Args : Bio::PrimarySeqI compliant object
=cut
sub mask{
return shift->run(@_);
}
=head2 _run
Title : _run
Usage : $rm->_run ($filename,$param_string)
Function: internal function that runs the repeat masker
Example :
Returns : an array of repeat features
Args : the filename to the input sequence and the parameter string
=cut
sub _run {
my ($self,$infile,$param_string) = @_;
my $instring;
$self->debug( "Program ".$self->executable."\n");
my $outfile = $infile.".out";
my $cmd_str = $self->executable." $param_string ". $infile;
$self->debug("repeat masker command = $cmd_str");
if ($self->quiet || $self->verbose <=0){
my $null = ($^O =~ m/mswin/i) ? 'NUL' : '/dev/null';
$cmd_str.=" 2> $null 1>$null";
}
my $status = system($cmd_str);
$self->throw("Repeat Masker Call($cmd_str) crashed: $?\n")
unless $status == 0;
unless (open (RM, $outfile)) {
$self->throw("Cannot open RepeatMasker outfile for parsing");
}
my $rpt_parser = Bio::Tools::RepeatMasker->new(-fh=>\*RM);
my @rpt_feat;
while(my $rpt_feat = $rpt_parser->next_result){
push @rpt_feat, $rpt_feat;
}
$self->repeat_features(\@rpt_feat);
#get masked sequence
my $masked = $infile.".masked";
my $seqio = Bio::SeqIO->new(-file=>$masked,-format=>'FASTA');
$self->masked_seq($seqio->next_seq);
return @rpt_feat;
}
=head2 masked_seq
Title : masked_seq
Usage : $rm->masked_seq($seq)
Function: get/set for masked sequence
Example :
Returns : the masked sequence
Args : Bio::Seq object
=cut
sub masked_seq {
my ($self,$seq) = @_;
if($seq){
$self->{'_masked_seq'} = $seq;
}
return $self->{'_masked_seq'};
}
=head2 repeat_features
Title : repeat_features
Usage : $rm->repeat_features(\@rf)
Function: get/set for repeat features array
Example :
Returns : the array of repeat features
Args :
=cut
sub repeat_features {
my ($self,$rf) = @_;
if($rf) {
$self->{'_rf'} = $rf;
}
return @{$self->{'_rf'}};
}
=head2 _setparams()
Title : _setparams
Usage : Internal function, not to be called directly
Function: Create parameter inputs for repeatmasker program
Example :
Returns : parameter string to be passed to repeatmasker
Args : name of calling object
=cut
sub _setparams {
my ($attr, $value, $self);
$self = shift;
my $param_string = "";
for $attr ( @RM_PARAMS ) {
$value = $self->$attr();
next unless (defined $value);
my $attr_key = lc $attr; #put params in format expected by dba
$attr_key = ' -'.$attr_key;
$param_string .= $attr_key.' '.$value;
}
for $attr ( @RM_SWITCHES) {
$value = $self->$attr();
next unless ($value);
my $attr_key = lc $attr; #put switches in format expected by dba
$attr_key = ' -'.$attr_key;
$param_string .= $attr_key ;
}
return $param_string;
}
=head2 _setinput()
Title : _setinput
Usage : Internal function, not to be called directly
Function: writes input sequence to file and return the file name
Example :
Returns : string
Args : a Bio::PrimarySeqI compliant object
=cut
sub _setinput {
my ($self,$seq) = @_;
$seq->isa("Bio::PrimarySeqI") ||
$self->throw("Need a Bio::PrimarySeq compliant object for RepeatMasker");
# my $in = Bio::SeqIO->new(-file => $infilename , '-format' => 'Fasta');
my ($tfh1,$outfile1) = $self->io->tempfile(-dir=>$self->tempdir);
my $out1 = Bio::SeqIO->new(-fh=> $tfh1 , '-format' => 'fasta');
$out1->write_seq($seq);
close($tfh1);
undef $tfh1;
return ($outfile1);
}
=head1 Bio::Tools::Run::Wrapper methods
=cut
=head2 no_param_checks
Title : no_param_checks
Usage : $obj->no_param_checks($newval)
Function: Boolean flag as to whether or not we should
trust the sanity checks for parameter values
Returns : value of no_param_checks
Args : newvalue (optional)
=cut
=head2 save_tempfiles
Title : save_tempfiles
Usage : $obj->save_tempfiles($newval)
Function:
Returns : value of save_tempfiles
Args : newvalue (optional)
=cut
=head2 outfile_name
Title : outfile_name
Usage : my $outfile = $codeml->outfile_name();
Function: Get/Set the name of the output file for this run
(if you wanted to do something special)
Returns : string
Args : [optional] string to set value to
=cut
=head2 tempdir
Title : tempdir
Usage : my $tmpdir = $self->tempdir();
Function: Retrieve a temporary directory name (which is created)
Returns : string which is the name of the temporary directory
Args : none
=cut
=head2 cleanup
Title : cleanup
Usage : $codeml->cleanup();
Function: Will cleanup the tempdir directory
Returns : none
Args : none
=cut
=head2 io
Title : io
Usage : $obj->io($newval)
Function: Gets a L<Bio::Root::IO> object
Returns : L<Bio::Root::IO>
Args : none
=cut
1;