# Wrapper module for Coil Bio::Tools::Run::Coil
#
# Based on the EnsEMBL module Bio::EnsEMBL::Pipeline::Runnable::Protein::Coil
# originally written by Marc Sohrmann (ms2@sanger.ac.uk)
# Written in BioPipe by Balamurugan Kumarasamy <savikalpa@fugu-sg.org>
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by the Fugu Informatics team (fuguteam@fugu-sg.org)
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
=head1 NAME
Bio::Tools::Run::Coil - wrapper for ncoils program
=head1 SYNOPSIS
# Build a Coil factory
my $factory = Bio::Tools::Run::Coil->new($params);
# Pass the factory a Bio::Seq object
# @feats is an array of Bio::SeqFeature::Generic objects
my @feats = $factory->run($seq);
=head1 DESCRIPTION
This module is a wrapper for the B<ncoils> program available via
L<http://www.russell.embl-heidelberg.de/coils/coils.tar.gz> for predicting
coiled coils in protein sequences.
By default it looks for an executable called I<ncoils> and data/parameter files
in the directory specified by the I<COILSDIR> environmental variable.
=head1 REFERENCES
Lupas, van Dyke & Stock,
I<Predicting coiled coils from protein sequences>,
Science B<252>:1162-1164, 1991.
Lupas, A.,
I<Prediction and Analysis of Coiled-Coil Structures>,
Meth. Enzymology B<266>:513-525, 1996.
=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 AUTHORS
Based on the EnsEMBL module Bio::EnsEMBL::Pipeline::Runnable::Protein::Coil
originally written by Marc Sohrmann (ms2@sanger.ac.uk)
Written in BioPipe by Balamurugan Kumarasamy <savikalpa@fugu-sg.org>
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
Cared for by the Fugu Informatics team (fuguteam@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::Coil;
use vars qw($AUTOLOAD @ISA $PROGRAM $PROGRAMDIR
$PROGRAMNAME @COIL_PARAMS %OK_FIELD);
use strict;
use Bio::SeqIO;
use Bio::Root::Root;
use Bio::Root::IO;
use Bio::Tools::Coil;
use Bio::Tools::Run::WrapperBase;
@ISA = qw(Bio::Root::Root Bio::Tools::Run::WrapperBase);
BEGIN {
@COIL_PARAMS=qw(PROGRAM VERBOSE QUIET SILENT);
foreach my $attr ( @COIL_PARAMS)
{ $OK_FIELD{$attr}++; }
}
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 program_name
Title : program_name
Usage : $factory>program_name()
Function: holds the program name
Returns: string
Args : None
=cut
sub program_name {
return 'ncoils';
}
=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{COILSDIR}) if $ENV{COILSDIR};
}
=head2 new
Title : new
Usage : $coil->new(@params)
Function: creates a new Coil factory
Returns: Bio::Tools::Run::Coil
Args :
=cut
sub new {
my ($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($attr, $value);
while (@args) {
$attr = shift @args;
$value = shift @args;
next if( $attr =~ /^-/ ); # don't want named parameters
if ($attr =~/PROGRAM/i) {
$self->executable($value);
next;
}
$self->$attr($value);
}
return $self;
}
=head2 predict_protein_features
Title : predict_protein_features()
Usage : DEPRECATED. Use $obj->run instead.
Function: Runs Coil and creates an array of featrues
Returns : An array of Bio::SeqFeature::Generic objects
Args : A Bio::PrimarySeqI
=cut
sub predict_protein_features{
return shift->run(@_);
}
=head2 run
Title : run
Usage : $obj->run($seq)
Function: Runs Coil and creates an array of featrues
Returns : An array of Bio::SeqFeature::Generic objects
Args : A Bio::PrimarySeqI, or a Fasta filename.
=cut
sub run{
my ($self,$seq) = @_;
my @feats;
if (ref($seq) ) { # it is an object
if (ref($seq) =~ /GLOB/) {
$self->throw("cannot use filehandle");
}
my $infile1 = $self->_writeSeqFile($seq);
$self->_input($infile1);
@feats = $self->_run();
unlink $infile1;
}
else {
#The argument is not a seq object but a sequence in a fasta file.
#Perhaps should check here or before if this file is fasta format...if not die
#Here the file does not need to be created or deleted. Its already written and may be used by other runnables.
$self->_input($seq);
@feats = $self->_run();
}
return @feats;
}
=head2 _input
Title : _input
Usage : obj->_input($seqFile)
Function: Internal(not to be used directly)
Returns :
Args :
=cut
sub _input() {
my ($self,$infile1) = @_;
if(defined $infile1){
$self->{'input'}=$infile1;
}
return $self->{'input'};
}
=head2 _run
Title : _run
Usage : $obj->_run()
Function: Internal(not to be used directly)
Returns : An array of Bio::SeqFeature::Generic objects
Args :
=cut
sub _run {
my ($self)= @_;
my ($tfh1,$outfile) = $self->io->tempfile(-dir=>$self->tempdir());
my $str =$self->executable." -f < ".$self->{'input'}." > ".$outfile;
if($self->quiet || $self->verbose <=0 || $self->silent){
my $null = ($^O =~ m/mswin/i) ? 'NUL' : '/dev/null';
$str.=" 2>$null";
}
my $status = system($str);
$self->throw( "Coil call ($str) crashed: $? \n") unless $status==0;
my $coil_parser = Bio::Tools::Coil->new();
my $filehandle;
if (ref ($outfile) !~ /GLOB/) {
open (COIL, "<".$outfile) or $self->throw ("Couldn't open file ".$outfile.": $!\n");
$filehandle = \*COIL;
}
else {
$filehandle = $outfile;
}
my @coil_feat;
while(my $coil_feat = $coil_parser->next_result($filehandle)){
push @coil_feat, $coil_feat;
}
$self->cleanup();
close($tfh1);
undef $tfh1;
unlink $outfile;
return @coil_feat;
}
=head2 _writeSeqFile
Title : _writeSeqFile
Usage : obj->_writeSeqFile($seq)
Function: Internal(not to be used directly)
Returns :
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');
$in->write_seq($seq);
return $inputfile;
}
1;