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   : 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

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

Methods code

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;
        }

}

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;

}

General documentation

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Additional contributors names and emails here

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