Bio::Tools::Profile - parse Profile output

 use Bio::Tools::Profile;
 my $profile_parser = Bio::Tools::Profile->new(-fh =>$filehandle );
 while( my $profile_feat = $profile_parser->next_result ) {
       push @profile_feat, $profile_feat;
}

 Parser for Profile output

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

 Title   : new
 Usage   : my $obj = Bio::Tools::Profile->new();
 Function: Builds a new Bio::Tools::Profile object
 Returns : Bio::Tools::Profile
 Args    : -filename
           -fh ($filehandle)

 Title   : next_result
 Usage   : my $feat = $profile_parser->next_result
 Function: Get the next result set from parser data
 Returns : L<Bio::SeqFeature::FeaturePair>
 Args    : none

 Title   : create_feature
 Usage   : my $feat= $profile_parser->create_feature($feature)
 Function: creates a Bio::SeqFeature::FeaturePair object
 Returns : L<Bio::SeqFeature::FeaturePair>
 Args    :

# BioPerl module for Bio::Tools::Profile
#
# Please direct questions and support issues to <bioperl-l@bioperl.org> 
#
# Cared for by Balamurugan Kumarasamy
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code

package Bio::Tools::Profile;
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 next_result {
        my ($self) = @_;

        my %printsac;
        my $line;
        my @features;
        while ($_=$self->_readline()) { 
                $line = $_;
                chomp $line;
                my ($nscore,$rawscore,$from,$to,$hfrom,$hto,$ac) = $line =~ /(\S+)\s+(\d+)\s*pos.\s+(\d*)\s*-\s+(\d*)\s*\[\s+(\d*),\s+(\S*)\]\s*(\w+)/;
                #for example in this output line 
                #38.435   2559 pos.  19958 - 20212 [    1,    -1] PS50011|PROTEIN_KINASE_DOM Protein kinase domain profile.
                #$nscore = 38.435
                #$rawscore = 2559
                #$from = 19958
                #$end = 20212
                #$hfrom = 1
                #$hto =-1
                #$ac = PS50011
                my $feat = "$ac,$from,$to,$hfrom,$hto,$nscore";
                my $new_feat= $self->create_feature($feat);
                return $new_feat

        } 
}

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

        my @f = split (/,/,$feat);


        my $hto = $f[4];

        if ($f[4] =~ /-1/) {
 
           $hto = $f[2] - $f[1] + 1;
        
        }


        my $feat1 = Bio::SeqFeature::Generic->new( -start => $f[1],
                                                   -end => $f[2],
                                                   -score => $f[5],
                                                   -source=>'pfscan',
                                                   -primary=>$f[0]);  
        
        my $feat2 = Bio::SeqFeature::Generic->new(-start => $f[3],
                                                  -end => $hto,
                                                  );  

        my $feature = Bio::SeqFeature::FeaturePair->new(-feature1 => $feat1,
                                                    -feature2 => $feat2);

        return $feature;
        
}
1;