Summary

Bio::Tools::Promoterwise - DESCRIPTION of Object

Package variables

Included modules

Inherit

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

Synopsis

  use Bio::Tools::Promoterwise;

  my $pw = Bio::Tools::Promoterwise->new(-file=>"out",
                                         -query1_seq=>$seq1,
                                         -query2_seq=>$seq2);
  while (my $fp = $pw->next_result){
    print "Hit Length: ".$fp->feature1->length."\n";
    print "Hit Start: ".$fp->feature1->start."\n";
    print "Hit End: ".$fp->feature1->end."\n";
    print "Hsps: \n";
    my @first_hsp = $fp->feature1->sub_SeqFeature;
    my @second_hsp = $fp->feature2->sub_SeqFeature;
    foreach my $i (0..$#first_hsp){
      print $first_hsp[$i]->start. " ".$first_hsp[$i]->end." ".
            $second_hsp[$i]->start. " ".$second_hsp[$i]->end."\n";
    }
  }

Description

Promoteriwise is an alignment algorithm that relaxes the constraint
that local alignments have to be co-linear. Otherwise it provides a
similar model to DBA, which is designed for promoter sequence
alignments. Promoterwise is written by Ewan Birney. It is part of
the wise2 package available at:
ftp://ftp.ebi.ac.uk/pub/software/unix/wise2/
This module is the parser for the Promoterwise output in tab format.

Methods

Methods description

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

 Title   : next_result
 Usage   : my $r = $rpt_masker->next_result
 Function: Get the next result set from parser data
 Returns : an  Bio::SeqFeature::FeaturePair
 Args    : none

Methods code

sub new {

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

  my $self = $class->SUPER::new(@args);
  $self->_initialize_io(@args);
  my ($query1,$query2) = $self->_rearrange([qw(QUERY1_SEQ QUERY2_SEQ)],@args);
  $self->query1_seq($query1) if ($query1);
  $self->query2_seq($query2) if ($query2);

  return $self;

}

sub next_result {

  my ($self) = @_;
  $self->_parse unless $self->_parsed;
  return $self->_next_result;

}

sub _parse {

   my ($self) = @_;
   my (%hash,@fp);
   while ($_=$self->_readline()) {
      chomp;
      my @array = split;
      push @{$hash{$array[$#array]}},\@ array;
   }
   foreach my $key(keys %hash){
    my $sf1 = Bio::SeqFeature::Generic->new(-primary=>"conserved_element",
                                            -source_tag=>"promoterwise");
    $sf1->attach_seq($self->query1_seq) if $self->query1_seq;
    my $sf2 = Bio::SeqFeature::Generic->new(-primary=>"conserved_element",
                                            -source_tag=>"promoterwise");
    $sf2->attach_seq($self->query2_seq) if $self->query2_seq;
    foreach my $info(@{$hash{$key}}){
      my ($score,$id1,$start_1,$end_1, $strand_1,$id2,$start_2,$end_2,
          $strand_2,$group)= @{$info};
      if(!$sf1->strand && !$sf2->strand){
        $sf1->strand($strand_1);
        $sf2->strand($strand_2);
        $sf1->seq_id($id1);
        $sf2->seq_id($id2);
        $sf1->score($score);
        $sf2->score($score);
      }
      my $sub1 = Bio::SeqFeature::Generic->new(-start=>$start_1,
                                              -seq_id=>$id1,
                                              -end  =>$end_1,
                                              -strand=>$strand_1,
                                              -primary=>"conserved_element",
                                              -source_tag=>"promoterwise",
                                              -score=>$score);
      $sub1->attach_seq($self->query1_seq) if $self->query1_seq;

      my $sub2 = Bio::SeqFeature::Generic->new(-start=>$start_2,
                                              -seq_id=>$id2,
                                              -end  =>$end_2,
                                              -strand=>$strand_2,
                                              -primary=>"conserved_element",
                                              -source_tag=>"promoterwise",
                                              -score=>$score);
      $sub2->attach_seq($self->query2_seq) if $self->query2_seq;
      $sf1->add_SeqFeature($sub1,'EXPAND');
      $sf2->add_SeqFeature($sub2,'EXPAND');
    }

    my $fp = Bio::SeqFeature::FeaturePair->new(-feature1=>$sf1,
                                               -feature2=>$sf2);
    push @fp, $fp;
  }
    $self->_feature_pairs(\@fp);
    $self->_parsed(1);
    return;

}

sub _feature_pairs {

  my ($self,$fp) = @_;
  if($fp){
    $self->{'_feature_pairs'} = $fp;
  }
  return  $self->{'_feature_pairs'};

}

sub _next_result {

  my ($self) = @_;
  return undef unless (exists($self->{'_feature_pairs'}) && @{$self->{'_feature_pairs'}});
  return shift(@{$self->{'_feature_pairs'}});

}

sub _parsed {

  my ($self,$flag) = @_;
  if($flag){
    $self->{'_flag'} = 1;
  }
  return $self->{'_flag'};

}

sub query1_seq {

  my ($self,$val) = @_;
  if($val){
    $self->{'query1_seq'} = $val;
  }
  return $self->{'query1_seq'};

}

sub query2_seq {

  my ($self,$val) = @_;
  if($val){
    $self->{'query2_seq'} = $val;
  }
  return $self->{'query2_seq'};

}

General documentation

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