view variant_effect_predictor/Bio/Tools/Promoterwise.pm @ 3:d30fa12e4cc5 default tip

Merge heads 2:a5976b2dce6f and 1:09613ce8151e which were created as a result of a recently fixed bug.

# BioPerl module for Bio::Tools::Promoterwise
#
# Cared for by Shawn Hoon <[e-mail]>
#
# Copyright Shawn Hoon
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code

=head1 NAME

Bio::Tools::Promoterwise - DESCRIPTION of Object

=head1 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";
    }
  }

=head1 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.

=head1 FEEDBACK

=head2 Mailing Lists

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.

  [e-mail]              - General discussion
  http://bioperl.org/MailList.shtml  - About the mailing lists

=head2 Reporting Bugs

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:

  [e-mail]
  http://bugzilla.bioperl.org/

=head1 AUTHOR - Shawn Hoon

Email [e-mail]

Describe contact details here

=head1 CONTRIBUTORS

Additional contributors names and emails here

=head1 APPENDIX

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

=cut


# Let the code begin...


package Bio::Tools::Promoterwise;
use vars qw(@ISA);
use strict;

use Bio::Root::Root;
use Bio::SeqFeature::FeaturePair;
use Bio::SeqFeature::Generic;
use Bio::Root::IO;

@ISA = qw(Bio::Root::Root Bio::Root::IO );

=head2 new

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


=cut

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;
}

=head2 next_result

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


=cut

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'};
}
1;