Bio::Tools Profile
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Summary
Bio::Tools::Profile - parse Profile output
Package variables
No package variables defined.
Included modules
Bio::SeqFeature::FeaturePair
Bio::SeqFeature::Generic
Inherit
Bio::Root::IO Bio::Root::Root
Synopsis
 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;
}
Description
 Parser for Profile output
Methods
newDescriptionCode
next_resultDescriptionCode
create_featureDescriptionCode
Methods description
newcode    nextTop
 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)
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 = 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;
}
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
Support Top
Please direct usage questions or support issues to the mailing list:
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.
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:
  https://redmine.open-bio.org/projects/bioperl/
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 _