view variant_effect_predictor/Bio/EnsEMBL/Analysis/PairAlign.pm @ 3:d30fa12e4cc5 default tip

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

=head1 LICENSE

  Copyright (c) 1999-2012 The European Bioinformatics Institute and
  Genome Research Limited.  All rights reserved.

  This software is distributed under a modified Apache license.
  For license details, please see

    http://www.ensembl.org/info/about/code_licence.html

=head1 CONTACT

  Please email comments or questions to the public Ensembl
  developers list at <[e-mail]>.

  Questions may also be sent to the Ensembl help desk at
  <[e-mail]>.

=cut

=head1 NAME

PairAlign - Dna pairwise alignment module

=head1 SYNOPSIS

#To convert between coordinates:

  my $cdna_coord = $pair->genomic2cDNA($gen_coord);
  my $gen_coord  = $pair->cDNA2genomic($cdna_coord);

=head1 DESCRIPTION

Contains list of sub alignments making up a dna-dna alignment

Creation:

  my $pair = new Bio::EnsEMBL::FeaturePair(
    -start  => $qstart,
    -end    => $qend,
    -strand => $qstrand,
    -hstart => $hstart,
    -hend   => $hend,
    -hend   => $hstrand,
  );

  my $pairaln = new Bio::EnsEMBL::Analysis::PairAlign;
  $pairaln->addFeaturePair($pair);

Any number of pair alignments can be added to the PairAlign object

=cut

package Bio::EnsEMBL::Analysis::PairAlign;

use vars qw(@ISA);
use strict;


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

sub new {
    my($class,@args) = @_;
    my $self = {};
    bless $self, $class;

    $self->{'_homol'} = [];
    
    return $self; # success - we hope!
}

sub addFeaturePair {
    my ($self,$pair) = @_;

    $self->throw("Not a Bio::EnsEMBL::FeaturePair object") unless ($pair->isa("Bio::EnsEMBL::FeaturePair"));

    push(@{$self->{'_pairs'}},$pair);
    
}


=head2 eachFeaturePair

 Title   : eachFeaturePair 
 Example : my @pairs = $pair->eachFeaturePair
 Returns : Array of Bio::SeqFeature::FeaturePair
 Args    : none
=cut

sub eachFeaturePair {
    my ($self) = @_;

    if (defined($self->{'_pairs'})) {
	return @{$self->{'_pairs'}};
    }
}

sub get_hstrand {
    my ($self) = @_;

    my @features = $self->eachFeaturePair;

    return $features[0]->hstrand;
}

=head2 genomic2cDNA

 Title   : genomic2cDNA
 Usage   : my $cdna_coord = $pair->genomic2cDNA($gen_coord)
 Function: Converts a genomic coordinate to a cdna coordinate
 Returns : int
 Args    : int
=cut

sub genomic2cDNA {
  my ($self,$coord) = @_;
  my @pairs = $self->eachFeaturePair;
  
  @pairs = sort {$a->start <=> $b->start} @pairs;
  
  my $newcoord;
  
  HOMOL: while (my $sf1 = shift(@pairs)) {
    next HOMOL unless ($coord >= $sf1->start && $coord <= $sf1->end);
    
    if ($sf1->strand == 1 && $sf1->hstrand == 1) {
      $newcoord = $sf1->hstart + ($coord - $sf1->start);
      last HOMOL;
    } elsif ($sf1->strand == 1 && $sf1->hstrand == -1) {
      $newcoord = $sf1->hend   - ($coord - $sf1->start);
      last HOMOL;
    } elsif ($sf1->strand == -1 && $sf1->hstrand == 1) {
      $newcoord = $sf1->hstart + ($sf1->end - $coord);
      last HOMOL;
    } elsif ($sf1->strand == -1 && $sf1->hstrand == -1) {
      $newcoord = $sf1->hend   - ($sf1->end - $coord);
      last HOMOL;
    } else {
      $self->throw("ERROR: Wrong strand value in FeaturePair (" . $sf1->strand . "/" . $sf1->hstrand . "\n");
    }
  }    
  
  if (defined($newcoord)) {
    
    return $newcoord;
  } else {
    $self->throw("Couldn't convert $coord");
  }
}

=head2 cDNA2genomic

 Title   : cDNA2genomic
 Usage   : my $gen_coord = $pair->genomic2cDNA($cdna_coord)
 Function: Converts a cdna coordinate to a genomic coordinate
 Example : 
 Returns : int
 Args    : int


=cut

sub cDNA2genomic {
  my ($self,$coord) = @_;
  
  my @pairs = $self->eachFeaturePair;
  
  my $newcoord;
  
  HOMOL: while (my $sf1 = shift(@pairs)) {
    next HOMOL unless ($coord >= $sf1->hstart && $coord <= $sf1->hend);
    
    if ($sf1->strand == 1 && $sf1->hstrand == 1) {
      $newcoord = $sf1->start + ($coord - $sf1->hstart);
      last HOMOL;
    } elsif ($sf1->strand == 1 && $sf1->hstrand == -1) {
      $newcoord = $sf1->start  +($sf1->hend - $coord);
      last HOMOL;
    } elsif ($sf1->strand == -1 && $sf1->hstrand == 1) {
      $newcoord = $sf1->end   - ($coord - $sf1->hstart);
      last HOMOL;
    } elsif ($sf1->strand == -1 && $sf1->hstrand == -1) {
      $newcoord = $sf1->end   - ($sf1->hend - $coord);
      last HOMOL; 
    } else {
      $self->throw("ERROR: Wrong strand value in homol (" . $sf1->strand . "/" . $sf1->hstrand . "\n");
    }
  }
  
  if (defined ($newcoord)) {
    return $newcoord;
  } else {
    $self->throw("Couldn't convert $coord\n");
  }
}

sub find_Pair {
  my ($self,$coord) = @_;
  
  foreach my $p ($self->eachFeaturePair) {
    if ($coord >= $p->hstart && $coord <= $p->hend) {
      return $p;
    }
  }
}

=head2 convert_cDNA_feature

 Title   : convert_cDNA_feature
 Usage   : my @newfeatures = $self->convert_cDNA_feature($f);
 Function: Converts a feature on the cDNA into an array of 
           features on the genomic (for features that span across introns);
 Returns : Array of Bio::EnsEMBL::FeaturePair
 Args    : Bio::EnsEMBL::FeaturePair

=cut

sub convert_cDNA_feature {
  my ($self,$feature) = @_;
    
  my $foundstart = 0;
  my $foundend   = 0;
  
  my @pairs = $self->eachFeaturePair;
  my @newfeatures;
  
  HOMOL: while (my $sf1 = shift(@pairs)) {
    my $skip = 0;
    #print STDERR "Looking at cDNA exon " . $sf1->hstart . "\t" . $sf1->hend . "\t" . $sf1->strand ."\n";
    
    $skip = 1 unless ($feature->start >= $sf1->hstart 
                      && $feature->start <= $sf1->hend);
    
    if($skip){
      #print STDERR "Skipping ".$sf1->hstart . "\t" . $sf1->hend . "\t" . $sf1->strand ."\n";
      next HOMOL;
    }
    if ($feature->end >= $sf1->hstart && $feature->end <= $sf1->hend) {
      $foundend = 1;
    }
    
    my $startcoord = $self->cDNA2genomic($feature->start);
    my $endcoord;
    
    if ($sf1->hstrand == 1) {
      $endcoord   = $sf1->end;
    } else {
      $endcoord   = $sf1->start;
    }
    
    if ($foundend) {
      $endcoord = $self->cDNA2genomic($feature->end);
    }
      
    #print STDERR "Making new genomic feature $startcoord\t$endcoord\n";
    
    my $tmpf = new Bio::EnsEMBL::Feature(-seqname => $feature->seqname,
                                            -start   => $startcoord,
                                            -end     => $endcoord,
                                            -strand  => $feature->strand);
    push(@newfeatures,$tmpf);
    last;
  }
    
  # Now the rest of the pairs until we find the endcoord
  
  while ((my $sf1 = shift(@pairs)) && ($foundend == 0)) {
    
    if ($feature->end >= $sf1->hstart && $feature->end <= $sf1->hend) {
      $foundend = 1;
    }
    
    my $startcoord;
    my $endcoord;
    
    if ($sf1->hstrand == 1) {
      $startcoord = $sf1->start;
      $endcoord   = $sf1->end;
    } else {
      $startcoord = $sf1->end;
      $endcoord   = $sf1->start;
    }
    
    if ($foundend) {
      $endcoord = $self->cDNA2genomic($feature->end);
    }
    
    #	#print STDERR "Making new genomic feature $startcoord\t$endcoord\n";
    
    my $tmpf = new Bio::EnsEMBL::Feature(-seqname => $feature->seqname,
                                         -start   => $startcoord,
                                         -end     => $endcoord,
                                         -strand  => $feature->strand);
    push(@newfeatures,$tmpf);
  }
  #print STDERR "Have ".@newfeatures." features from ".$feature."\n";
  return @newfeatures;
}


sub convert_FeaturePair {
  my ($self,$pair) = @_;

  my $hstrand = $self->get_hstrand;
  
  my $feat = $self->create_Feature($pair->start, $pair->end, $pair->strand,
                                   $pair->slice);
  my @newfeatures = $self->convert_cDNA_feature($feat);
  my @newpairs;
  
  my $hitpairaln  = new Bio::EnsEMBL::Analysis::PairAlign;
  $hitpairaln->addFeaturePair($pair);
  
  foreach my $new (@newfeatures) {
    
    # Now we want to convert these cDNA coords into hit coords
    
    my $hstart1 = $self->genomic2cDNA($new->start);
    my $hend1   = $self->genomic2cDNA($new->end);
    
    my $hstart2 = $hitpairaln->genomic2cDNA($hstart1);
    my $hend2   = $hitpairaln->genomic2cDNA($hend1);
    
    # We can now put the final feature together
    
    my $finalstrand = $hstrand * $pair->strand * $pair->hstrand;
    
    if ($hstart2 > $hend2) {
      my $tmp = $hstart2;
      $hstart2 = $hend2;
      $hend2   = $tmp;
    }
    
    my $finalpair = $self->create_FeaturePair($new->start, $new->end, 
                                              $new->strand,
                                              $hstart2, $hend2, 
                                              $finalstrand, $pair->score);
    
    push(@newpairs,$finalpair);
    
  }
  
  return @newpairs;
}

sub create_FeaturePair {
    my ($self, $start, $end, $strand, $hstart, $hend, 
        $hstrand, $score) = @_;
   
    my $fp = Bio::EnsEMBL::FeaturePair->new(
                                            -start    => $start,
                                            -end      => $end,
                                            -strand   => $strand,
                                            -hstart   => $hstart,
                                            -hend     => $hend,
                                            -hstrand  => $hstrand,
                                            -score    => $score,
                                           );

   
    return $fp;
}

sub create_Feature{
  my ($self, $start, $end, $strand,  $slice) = @_;

  my $feat = new Bio::EnsEMBL::Feature(-start   => $start,
                                       -end     => $end,
                                       -strand  => $strand,
                                       -slice   => $slice,
                                      );
  return $feat;
}

1;