libbio-perl-perl 1.6.924-1 / usr / share / perl5 / Bio / Tools / Prints.pm

#
# BioPerl module for Bio::Tools::Prints
#
# 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
#

=head1 NAME

Bio::Tools::Prints - Parser for FingerPRINTScanII program 

=head1 SYNOPSIS

  use Bio::Tools::Prints;
  my $prints_parser = Bio::Tools::Prints->new(-fh =>$filehandle );
  while( my $prints_feat = $prints_parser->next_result ) {
        push @prints_feat, $prints_feat;
  }

=head1 DESCRIPTION

 PRINTScan II is a PRINTS fingerprint identification algorithm.
 Copyright (C) 1998,1999  Phil Scordis

=head1 FEEDBACK

=head2 Mailing Lists

 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

=head2 Support 

Please direct usage questions or support issues to the mailing list:

I<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.

=head2 Reporting Bugs

 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://github.com/bioperl/bioperl-live/issues

=head1 AUTHOR - Balamurugan Kumarasamy

 bala@tll.org.sg
 juguang@tll.org.sg

=head1 APPENDIX

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


=cut

package Bio::Tools::Prints;
use strict;

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


=head2 new

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

=cut

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

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

      return $self;
}


=head2 next_result

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

=cut

sub next_result {
    my ($self) = @_;
    my %printsac;
    my @features;
    my $line;
    my $sequenceId;
     
    while ($_=$self->_readline()) {
      
           $line = $_;
           chomp $line;

           if ($line =~ s/^Sn;//) { # We have identified a Sn; line so there should be the following:

              ($sequenceId) = $line =~ /^\s*(\w+)/;
              $self->seqname($sequenceId);
              next;
           }
              
           if ($line =~ s/^1TBH//) {
               my  ($id) = $line =~ /^\s*(\w+)/;
               my ($ac) = $line =~ /(PR\w+)\s*$/;
               $printsac{$id} = $ac;
               $self->print_sac(\%printsac);
               next;
           }
             
           if ($line =~ s/^3TB//) {
              
              if ($line =~ s/^[HN]//) {
                   my($num)="";
                   $line =~ s/^\s+//;

                   my @elements = split /\s+/, $line;

                   my ($fingerprintName,$motifNumber,$temp,$tot,$percentageIdentity,$profileScore,$pvalue,$subsequence,$motifLength,$lowestMotifPosition,$matchPosition,$highestMotifPosition) = @elements;
    
                   my $start = $matchPosition;
                   my $end = $matchPosition + $motifLength - 1;
                   my $print_sac = $self->print_sac;
                   
                   my %printsac =  %{$print_sac};
                   my $print =  $printsac{$fingerprintName};
                   my $seqname=$self->seqname;
                   my $feat = "$print,$start,$end,$percentageIdentity,$profileScore,$pvalue";
                   my $new_feat =  $self->create_feature($feat,$seqname);
                   return $new_feat;
               }
               if ($line =~ s/^F//) {
                   return;  
               }
                   next;                                                       
               }
            next;         
 
      }

}

=head2 create_feature

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


=cut

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

    my @f = split (/,/,$feat);
    # create feature object
    my $feature= Bio::SeqFeature::Generic->new(
        -seq_id    =>$sequenceId,
        -start=>$f[1],
        -end  => $f[2],
        -score      => $f[4],
        -source     => "PRINTS",
        -primary    =>$f[0],
        -logic_name => "PRINTS",
    );
    $feature->add_tag_value('evalue',$f[5]);
    $feature->add_tag_value('percent_id',$f[3]);
        
    my $feature2 = Bio::SeqFeature::Generic->new(
        -seq_id => $f[0],
        -start => 0,
        -end => 0,
    );
    my $fp = Bio::SeqFeature::FeaturePair->new(
        -feature1 => $feature,
        -feature2 => $feature2
    );
    return  $fp; 
}

=head2 print_sac

 Title   : print_sac
 Usage   : $prints_parser->print_sac($print_sac)
 Function: get/set for print_sac
 Returns :
 Args    :


=cut

sub print_sac {
    my $self = shift;
    return $self->{'print_sac'} = shift if @_;
    return $self->{'print_sac'};
}

=head2 seqname 

 Title   : seqname
 Usage   : $prints_parser->seqname($seqname)
 Function: get/set for seqname
 Returns :
 Args    :


=cut

sub seqname {
    my($self,$seqname)=@_;
    return $self->{'seqname'}=$seqname if(defined($seqname));
    return $self->{'seqname'};
}

1;