speelink fixes, patch courtesy Charles Plessy, fixes #3256

[bioperl-run.git] / lib / Bio / Tools / Run / Coil.pm

# 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){
         $str.=" 2>/dev/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;