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Summary

Bio::Tools::Promoterwise - parser for Promoterwise tab format output

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 = Bio::Tools::Promoterwise->new();
 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 ($self) = @_;
   my (%hash,@fp);
   while (defined($_ = $self->_readline()) ) {
       chomp;
       my @array = split;
       push @{$hash{$array[-1]}},\@ 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, $strand_1,$s1_len,
	  $id2,$start_2,$end_2,$strand_2,$s2_len, $group);
      if( @{$info} == 12 ) {
	  ($score,$id1,$start_1,$end_1, $strand_1,$s1_len,
	   $id2,$start_2,$end_2,$strand_2,$s2_len, $group) = @{$info};
      } elsif( @{$info} == 10 ) {
	  ($score,$id1,$start_1,$end_1, $strand_1,
	   $id2,$start_2,$end_2,$s2_len, $group) = @{$info};
      } else {
	  $self->throw("unknown promoterwise output, ", scalar @{$info},
		       " columns, expected 10 or 12\n");
      }
      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 ($self) = @_;
  return unless (exists($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'};
}
1;

}

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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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.

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/

Email shawnh@fugu-sg.org

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