Bio::Tools::Coil - parser for Coil output

 use Bio::Tools::Coil
 my $parser = Bio::Tools::Coil->new();
 while( my $sp_feat = $parser->next_result($file) ) {
       #do something
       #eg
       push @sp_feat, $sp_feat;
 }

 Parser for Coil output

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 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)

 The rest of the documentation details each of the object methods.
 Internal methods are usually preceded with a _

 Title   : parse_results
 Usage   : obj->parse_results
 Function: Parses the coil output. Automatically called by
           next_result() if not yet done.
 Example :
 Returns :

 Title   : next_result
 Usage   : while($feat = $coil->next_result($file)) {
                  # do something
           }
 Function: Returns the next protein feature of the coil output file
 Returns : 
 Args    :

 Title   : _result
 Usage   : $feat = $obj->_result()
 Function: internal
 Example :
 Returns :

 Title   : _add_prediction()
 Usage   : $obj->_add_prediction($feat)
 Function: internal
 Example :
 Returns :

 Title   : _predictions_parsed
 Usage   : $obj->_predictions_parsed
 Function: internal
 Example :
 Returns : TRUE or FALSE

 Title   : create_feature
 Usage   : obj->create_feature(\%feature)
 Function: Internal(not to be used directly)
 Returns :
 Args    :

 Title   : _read_fasta
 Usage   : obj->_read_fasta($file)
 Function: Internal(not to be used directly)
 Returns :
 Args    :

# Parser module for Coil Bio::Tools::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

package Bio::Tools::Coil;
use strict;

use Bio::SeqFeature::FeaturePair;
use Bio::SeqFeature::Generic;
use base qw(Bio::Root::Root Bio::Root::IO);



sub new {
    my($class,@args) = @_;

    my $self = $class->SUPER::new(@args);
    $self->_initialize_io(@args);

    return $self;
}

sub parse_results {
    my ($self,$resfile) = @_;
    my $filehandle = $resfile;
    my %result_hash =_read_fasta($filehandle);#bala no file handle
        my @ids = keys %result_hash;
    my @feats; 
    foreach my $id (keys %result_hash){      
	my $pep = reverse ($result_hash{$id});
	my $count = my $switch = 0;
	my ($start, $end);
	while (my $aa = chop $pep) {
	    $count++;
	    if (!$switch && $aa eq "x") {
		$start = $count;
		$switch = 1;
	    }
	    elsif ($switch && $aa ne "x") {
		$end = $count-1;
		my (%feature);
		$feature{name}       = $id;
		$feature{start}      = $start;
		$feature{end}        = $end;
		$feature{source}     = "Coils";
		$feature{primary}    = 'ncoils';
		($feature{program})   = 'ncoils';
		$feature{logic_name} = 'Coils';
		my $new_feat = $self->create_feature (\%feature);
		$self->_add_prediction($new_feat);
		$switch = 0;
	    }
	}
    }

    $self->_predictions_parsed(1);

}

sub next_result {

    my ($self,$resfile) = @_;
    my $gene;

    $self->parse_results($resfile) unless $self->_predictions_parsed();

    $gene = $self->_result();

    return $gene;

}

sub _result {
    my ($self) = @_;

    return unless(exists($self->{'_feats'}) && @{$self->{'_feats'}});
    return shift(@{$self->{'_feats'}});
}

sub _add_prediction {
    my ($self, $gene) = @_;

    if(! exists($self->{'_feats'})) {
        $self->{'_feats'} = [];
    }
    push(@{$self->{'_feats'}}, $gene);
}

sub _predictions_parsed {
    my ($self, $val) = @_;

    $self->{'_preds_parsed'} = $val if $val;
    if(! exists($self->{'_preds_parsed'})) {
        $self->{'_preds_parsed'} = 0;
    }
    return $self->{'_preds_parsed'};
}

sub create_feature {
    my ($self, $feat) = @_;


    # create feature object
    my $feature = Bio::SeqFeature::Generic->new
	(-seq_id     => $feat->{name},
	 -start       => $feat->{start},
	 -end         => $feat->{end},
	 -score       => $feat->{score},
	 -source      => $feat->{source},
	 -primary     => $feat->{primary},
	 -logic_name  => $feat->{logic_name}, 
	 );
    $feature->add_tag_value('evalue',0);
    $feature->add_tag_value('percent_id','NULL');
    $feature->add_tag_value("hid",$feat->{primary});


    return $feature;

}

sub _read_fasta {
    local (*FILE) = @_;
    my( $id , $seq , %name2seq);#bala
        while (<FILE>) {
	    chomp;		#bala
	    if (/^>(\S+)/) {

		my $new_id = $1;
		if ($id) {
		    $name2seq{$id} = $seq;
		}
		$id = $new_id ; $seq = "" ;
	    } elsif (eof) {
		if ($id) {
		    $seq .= $_ ;#bala line instead of $_
		    $name2seq{$id} = $seq;
		}
	    }
	    else {
		$seq .= $_;
	    }
        }
    return %name2seq;
}

1;