Bio::Tools Profile
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Summary
Bio::Tools::Profile - parse Profile output
Package variables
No package variables defined.
Included modules
Bio::Root::IO
Bio::Root::Root
Bio::SeqFeature::FeaturePair
Bio::SeqFeature::Generic
Inherit
Bio::Root::IO Bio::Root::Root
Synopsis
 use Bio::Tools::Profile;
 my $profile_parser = new Bio::Tools::Profile(-fh =>$filehandle );
 while( my $profile_feat = $profile_parser->next_result ) {
       push @profile_feat, $profile_feat;
}
Description
 Parser for Profile output
Methods
newDescriptionCode
next_resultDescriptionCode
create_featureDescriptionCode
Methods description
newcode    nextTop
 Title   : new
 Usage   : my $obj = new Bio::Tools::Profile();
 Function: Builds a new Bio::Tools::Profile object
 Returns : Bio::Tools::Profile
 Args    : -filename
           -fh ($filehandle)
next_resultcodeprevnextTop
 Title   : next_result
 Usage   : my $feat = $profile_parser->next_result
 Function: Get the next result set from parser data
 Returns : Bio::SeqFeature::FeaturePair
 Args    : none
create_featurecodeprevnextTop
 Title   : create_feature
 Usage   : my $feat= $profile_parser->create_feature($feature)
 Function: creates a Bio::SeqFeature::FeaturePair object
 Returns : Bio::SeqFeature::FeaturePair
 Args    :
Methods code
newdescriptionprevnextTop
sub new {
    my($class,@args) = @_;

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

    return $self;
}
next_resultdescriptionprevnextTop
sub next_result {
        my ($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

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

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

        return $feature;
}
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/MailList.shtml  - 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
 email or the web:

 bioperl-bugs@bioperl.org
 http://bugzilla.bioperl.org/
AUTHOR - Balamurugan KumarasamyTop
 Email: fugui@worf.fugu-sg.org
APPENDIXTop
 The rest of the documentation details each of the object methods.
 Internal methods are usually preceded with a _