Bio::Tools Promoterwise
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Summary
Bio::Tools::Promoterwise - parser for Promoterwise tab format output
Package variables
No package variables defined.
Included modules
Bio::SeqFeature::FeaturePair
Bio::SeqFeature::Generic
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
newDescriptionCode
next_resultDescriptionCode
_parse
No description
Code
_feature_pairs
No description
Code
_next_result
No description
Code
_parsed
No description
Code
query1_seq
No description
Code
query2_seq
No description
Code
Methods description
newcode    nextTop
 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
next_resultcodeprevnextTop
 Title   : next_result
Usage : my $r = $rpt_masker->next_result
Function: Get the next result set from parser data
Returns : an Bio::SeqFeature::FeaturePair
Args : none
Methods code
newdescriptionprevnextTop
sub new {
  my($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 $self;
}
next_resultdescriptionprevnextTop
sub next_result {
  my ($self) = @_;
  $self->_parse unless $self->_parsed;
  return $self->_next_result;
}
_parsedescriptionprevnextTop
sub _parse {
   my ($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);
    $self->_parsed(1);
    return;
}
_feature_pairsdescriptionprevnextTop
sub _feature_pairs {
  my ($self,$fp) = @_;
  if($fp){
    $self->{'_feature_pairs'} = $fp;
  }
  return  $self->{'_feature_pairs'};
}
_next_resultdescriptionprevnextTop
sub _next_result {
  my ($self) = @_;
  return unless (exists($self->{'_feature_pairs'}) && @{$self->{'_feature_pairs'}});
  return shift(@{$self->{'_feature_pairs'}});
}
_parseddescriptionprevnextTop
sub _parsed {
  my ($self,$flag) = @_;
  if($flag){
    $self->{'_flag'} = 1;
  }
  return $self->{'_flag'};
}
query1_seqdescriptionprevnextTop
sub query1_seq {
  my ($self,$val) = @_;
  if($val){
    $self->{'query1_seq'} = $val;
  }
  return $self->{'query1_seq'};
}
query2_seqdescriptionprevnextTop
sub query2_seq {
  my ($self,$val) = @_;
  if($val){
    $self->{'query2_seq'} = $val;
  }
  return $self->{'query2_seq'};
}
1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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
Support Top
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.
Reporting BugsTop
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/
AUTHOR - Shawn HoonTop
Email shawnh@fugu-sg.org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _