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Summary

MiniSeq - an artificially constructed cDNA on a genomic sequence

Package variables

Included modules

Inherit

Synopsis

This module is used when we only want to run an analysis over
a part or multiple parts of a sequence.

Description

Contains details of coordinates of all exons that make
up a gene transcript.
Creation:

my $mini = new Bio::EnsEMBL::Analysis::Tools::MiniSeq(-id => $id,
-pairaln => $pairaln);

   $pairaln is a Bio::EnsEMBL::Analysis::PairAlign object containing
   one or more feature pairs that represent the mapping of
   the genomic coords to the cDNA coords

Manipulation:

    my $align   = $mini->get_PairAlign;
    my $cdnaseq = $mini->get_cDNA_sequence;

# We now do some analysis on the cdnaseq that puts sequence
# features on it. We don't want the coordsin the cDNA frame so
# we now pass them back to the miniseq to convert them into
# genomic coordinates.

    my  @newfeatures = $mini->convert_FeaturePairs(@featurepairs);

Methods

Methods description

 Title   : convert_FeaturePair
 Usage   : my @newfeatures = $self->convert_FeaturePairs($feature)
 Function: Converts feature pair coordinates on the cDNA sequence
           into an array of feature pairs on the genomic sequence
 Example : 
 Returns : Bio::EnsEMBL::FeaturePair
 Args    : Array of Bio::EnsEMBL::FeaturePair

 Title   : convert_PepFeaturePair
 Usage   : my @newfeatures = $self->convert_PepFeaturePair($feature)
 Function: Converts feature pair coordinates on the cDNA sequence
           into an array of feature pairs on the genomic sequence
           Peptide coordinates are maintained.
 Example : 
 Returns : Array of Bio::EnsEMBL::FeaturePair
 Args    : Bio::EnsEMBL::FeaturePair

 Title   : convert_FeaturePair
 Usage   : my @newfeatures = $self->convert_FeaturePairs($feature)
 Function: Converts feature coordinates on the cDNA sequence
           into an array of features on the genomic sequence
 Example : 
 Returns : Bio::EnsEMBL::FeaturePair
 Args    : Array of Bio::EnsEMBL::FeaturePair

 Title   : get_cDNA_sequence
 Usage   : my $seq = $self->get_cDNA_sequence
 Function: Returns the cdna sequence corresponding
           to the cDNA in the pairAlign object
 Example : 
 Returns : Bio::PrimarySeq
 Args    : none

 Title   : id
 Usage   : $obj->id($newval)
 Function: 
 Returns : value of id
 Args    : newvalue (optional)

 Title   : pairAlign
 Usage   : $self->pairAlign($pair)
 Function: Get/set method for the pairalign object
           that stores the cDNA-genomic exon mapping
 Returns : Bio::EnsEMBL::Analysis::PairAlign
 Args    :

Methods code

sub convert_FeaturePair {

    my ($self,$feature) = @_;

    my @newfeatures;

    my @tmp = @{$self->pairAlign->convert_FeaturePair($feature)};
    push(@newfeatures,@tmp);

    return\@ newfeatures;

}

sub convert_PepFeaturePair {

    my ($self,$feature) = @_;

    my @newfeatures;

    my @tmp = @{$self->pairAlign->convert_FeaturePair($feature)};

    # replace protein coordinates
    $tmp[0]->hstart($feature->hstart);
    $tmp[0]->hend($feature->hend);
# SMJS strand of peptide should be positive?
    $tmp[0]->hstrand(1);

    push(@newfeatures,@tmp);

    return\@ newfeatures;
}

1;

}

sub convert_SeqFeature {

    my ($self,$feature) = @_;

    my @newfeatures;

    my @tmp = @{$self->pairAlign->convert_cDNA_feature($feature)};
    push(@newfeatures,@tmp);

    return\@ newfeatures;

}

sub get_cDNA_sequence {

  my ($self) = @_;

  my $seqstr = "";

  my @exons = @{$self->pairAlign->eachFeaturePair};
  return unless (scalar @exons > 0);

  foreach my $exon (@exons) {
    $seqstr .= $exon->seq;
  }
  return new Bio::PrimarySeq('-id' => "genomic" ,
                             -seq => $seqstr);

}

sub id {

  my ($self,$arg) = @_;

  if(defined($arg)) {
    $self->{'_id'} = $arg;
  }

  return $self->{'_id'};

}

sub new {

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

  my ($id,$pairalign) = rearrange([qw(ID PAIRALIGN)],@args);
  verbose('warning');
  #No defaults

  $self->id($id);
  $self->pairAlign($pairalign);

  throw("No input id for MiniSeq")        unless($self->id);
  throw("No input pairalign for MiniSeq") unless($self->pairAlign);

  
  return $self;

}

sub pairAlign {

  my ($self,$pair) = @_;

  if ($pair) {
    if( ! $pair->isa("Bio::EnsEMBL::Analysis::Tools::PairAlign") ) {
      throw("$pair is not a Bio::EnsEMBL::Analysis::Tools::PairAlign!");
    }
    foreach my $p (@{$pair->eachFeaturePair}) {
      if ($p->strand != 1) {
        throw("Can't have a PairAlign object where the strand of the first ".
              "object is reversed");
      }
    }
    $self->{'_pair'} = $pair;
  }
  return $self->{'_pair'};

}

General documentation

Describe contact details here

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