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Summary

Bio::Tools::Seg - parse Seg output (filter low complexity protein sequence)

Package variables

Included modules

Inherit

Bio::Root::IO Bio::Root::Root

Synopsis

  use Bio::Tools::Seg;
  my $parser = new Bio::Tools::Seg(-fh =>$filehandle );
  while( my $seg_feat = $parser->next_result ) {
        #do something
        #eg
        push @seg_feat, $seg_feat;
  }

Description

Parser for Seg output

Methods

Methods description

 Title   : create_feature
 Usage   : obj->create_feature(\%feature)
 Function: Internal(not to be used directly)
 Returns : 
 Args    :

 Title   : new
 Usage   : my $obj = new Bio::Tools::Seg();
 Function: Builds a new Bio::Tools::Seg object
 Returns : Bio::Tools::Seg
 Args    : -fh/-file => $val, # for initing input, see Bio::Root::IO

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

Methods code

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}, 
                                               );

          return $feature;

}

1;

}

sub new {

      my($class,@args) = @_;

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

      return $self;

}

sub next_result {

        my ($self) = @_;

        my $line;
        # parse
        my $id;
        while ($_=$self->_readline()) {
         $line = $_;
         chomp $line;

          next if /^$/;
           if ($line=~/^\>/) { #if it is a line starting with a ">"
               $line=~/^\>\s*(\S+)\s*\((\d+)\-(\d+)\)\s*complexity=(\S+)/;
               my $id = $1;
               my $start = $2;
               my $end = $3;
               my $score = $4;

               #for example in this line test_prot(214-226) complexity=2.26 (12/2.20/2.50)
               #$1 is test_prot  $2 is 214 $3 is 226 and $4 is 2.26

               my (%feature);
               $feature{name} = $id;
               $feature{score} = $score;
               $feature{start} = $start;
               $feature{end} = $end;
               $feature{source} = "Seg";
               $feature{primary} = 'low_complexity';
               $feature{program} = "Seg";
               $feature{logic_name} = 'low_complexity';
               my $new_feat =  $self->create_feature (\%feature);
               return $new_feat;
            }
          next;
        }

}

General documentation

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.

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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/

Email savikalpa@fugu-sg.org

Additional contributors names and emails here

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