Bio::Tools Coil
SummaryPackage variablesSynopsisDescriptionGeneral documentationMethods
Summary
Bio::Tools::Coil - parser for Coil output
Package variables
No package variables defined.
Included modules
Bio::SeqFeature::FeaturePair
Bio::SeqFeature::Generic
base qw ( Bio::Root::Root Bio::Root::IO )
Synopsis
 use Bio::Tools::Coil
 my $parser = new Bio::Tools::Coil();
 while( my $sp_feat = $parser->next_result($file) ) {
       #do something
       #eg
       push @sp_feat, $sp_feat;
 }
Description
 Parser for Coil output
Methods
new
No description
Code
parse_resultsDescriptionCode
next_resultDescriptionCode
_resultDescriptionCode
_add_predictionDescriptionCode
_predictions_parsedDescriptionCode
create_featureDescriptionCode
_read_fastaDescriptionCode
Methods description
parse_resultscode    nextTop
 Title   : parse_results
 Usage   : obj->parse_results
 Function: Parses the coil output. Automatically called by
           next_result() if not yet done.
 Example :
 Returns :
next_resultcodeprevnextTop
 Title   : next_result
 Usage   : while($feat = $coil->next_result($file)) {
                  # do something
           }
 Function: Returns the next protein feature of the coil output file
 Returns : 
 Args    :
_resultcodeprevnextTop
 Title   : _result
 Usage   : $feat = $obj->_result()
 Function: internal
 Example :
 Returns :
_add_predictioncodeprevnextTop
 Title   : _add_prediction()
 Usage   : $obj->_add_prediction($feat)
 Function: internal
 Example :
 Returns :
_predictions_parsedcodeprevnextTop
 Title   : _predictions_parsed
 Usage   : $obj->_predictions_parsed
 Function: internal
 Example :
 Returns : TRUE or FALSE
create_featurecodeprevnextTop
 Title   : create_feature
 Usage   : obj->create_feature(\%feature)
 Function: Internal(not to be used directly)
 Returns :
 Args    :
_read_fastacodeprevnextTop
 Title   : _read_fasta
 Usage   : obj->_read_fasta($file)
 Function: Internal(not to be used directly)
 Returns :
 Args    :
Methods code
newdescriptionprevnextTop
sub new {
    my($class,@args) = @_;

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

    return $self;
}
parse_resultsdescriptionprevnextTop
sub parse_results {
    my ($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;
	    }
	}
    }

    $self->_predictions_parsed(1);
}
next_resultdescriptionprevnextTop
sub next_result {
    my ($self,$resfile) = @_;
    my $gene;

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

    $gene = $self->_result();

    return $gene;
}
_resultdescriptionprevnextTop
sub _result {
    my ($self) = @_;

    return unless(exists($self->{'_feats'}) && @{$self->{'_feats'}});
    return shift(@{$self->{'_feats'}});
}
_add_predictiondescriptionprevnextTop
sub _add_prediction {
    my ($self, $gene) = @_;

    if(! exists($self->{'_feats'})) {
        $self->{'_feats'} = [];
    }
    push(@{$self->{'_feats'}}, $gene);
}
_predictions_parseddescriptionprevnextTop
sub _predictions_parsed {
    my ($self, $val) = @_;

    $self->{'_preds_parsed'} = $val if $val;
    if(! exists($self->{'_preds_parsed'})) {
        $self->{'_preds_parsed'} = 0;
    }
    return $self->{'_preds_parsed'};
}
create_featuredescriptionprevnextTop
sub create_feature {
    my ($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;
}
_read_fastadescriptionprevnextTop
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;
}
General documentation
FEEDBACKTop
Mailing ListsTop
 User feedback is an integral part of the evolution of this and other
 Bioperl modules. Send your comments and suggestions preferably to
 the Bioperl mailing list.  Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:
  http://bugzilla.open-bio.org/
AUTHORTop
 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>
 Cared for by the Fugu Informatics team (fuguteam@fugu-sg.org)
APPENDIXTop
 The rest of the documentation details each of the object methods.
 Internal methods are usually preceded with a _