diff variant_effect_predictor/Bio/EnsEMBL/PaddedSlice.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/PaddedSlice.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,228 @@
+=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
+
+Bio::EnsEMBL::PaddedSlice
+
+=head1 DESCRIPTION
+
+Used when dumping Slices which represet a portion of the sequence region
+they map to e.g. the first section of human Y. The code will return N
+as sequence if an attempt is made to retrieve sequence not covered by the
+Slice given. This makes the code very memory efficient if sequence dumping
+is carried out using C<subseq()> calls.
+
+=head1 METHODS
+
+=cut
+
+package Bio::EnsEMBL::PaddedSlice;
+
+use Bio::EnsEMBL::Utils::Argument qw/rearrange/;
+use Bio::EnsEMBL::Utils::Scalar qw/assert_ref assert_strand/;
+use base qw/Bio::EnsEMBL::Utils::Proxy/;
+
+=head2 new()
+
+  Arg [SLICE] : The Slice to proxy  
+  Example     : my $newobj = Bio::EnsEMBL::PaddedSlice->new($myobj);
+  Description : Provides a new instance of a padded slice
+  Returntype  : Bio::EnsEMBL::PaddedSlice
+  Exceptions  : None 
+  Caller      : public
+  Status      : -
+
+=cut
+
+sub new {
+  my ($class, @args) = @_;
+  my ($slice) = rearrange([qw/slice/], @args);
+  return $class->SUPER::new($slice);
+}
+
+=head2 start()
+
+  Example     : $slice->start();
+  Description : Always returns 1 since all padded slices start at 1
+  Returntype  : Int
+  Exceptions  : None 
+  Caller      : public
+  Status      : -
+
+=cut
+
+sub start {
+  my ($self) = @_;
+  return 1;
+}
+
+=head2 end()
+  
+  Example     : $slice->end();
+  Description : Always returns the backing slice sequence region length
+  Returntype  : Int
+  Exceptions  : None 
+  Caller      : public
+  Status      : -
+
+=cut
+
+sub end {
+  my ($self) = @_;
+  return $self->seq_region_length();
+}
+
+=head2 length()
+  
+  Example     : $slice->length();
+  Description : Delegates to C<end()>
+  Returntype  : Int
+  Exceptions  : None 
+  Caller      : public
+  Status      : -
+
+=cut
+
+sub length {
+  my ($self) = @_;
+  return $self->end();
+}
+
+=head2 seq()
+  
+  Example     : my $seq = $slice->seq()
+  Description : Returns the entire sequence of the backing slice but padded
+                with N's at the beginning and the end of the slice where
+                applicable
+  Returntype  : Scalar string
+  Exceptions  : None 
+  Caller      : public
+  Status      : -
+
+=cut
+
+sub seq {
+  my ($self) = @_;
+  my $parent_slice = $self->__proxy();
+  my $pad_start = 'N' x ( $parent_slice->start() - 1 );
+  my $pad_end   = 'N' x ( $parent_slice->seq_region_length() - $parent_slice->end() );
+  my $seq = $parent_slice->seq();
+  return $pad_start . $seq . $pad_end;
+}
+
+=head2 subseq()
+  
+  Arg [1]     : Int; start position of the subslice
+  Arg [2]     : Int; end position of the subslice
+  Arg [3]     : Int; strand of the subslice  
+  Example     : my $subseq = $slice->subseq(1, 1_000_000);
+  Description : Returns a portion of the sequence padded with N's if required 
+  Returntype  : Scalar string
+  Exceptions  : None 
+  Caller      : public
+  Status      : -
+
+=cut
+
+sub subseq {
+  my ( $self, $start, $end, $strand ) = @_;
+
+  if ( $end+1 < $start ) {
+    throw("End coord + 1 is less than start coord");
+  }
+  
+  return '' if( $start == $end + 1);
+  
+  $strand = 1 unless(defined $strand);
+  assert_strand($strand, 'strand');
+  
+  my $parent_slice = $self->__proxy();
+    
+  #Coords relative to the SeqRegion i.e. huge
+  my $parent_start = $parent_slice->start();
+  my $parent_end = $parent_slice->end();
+  
+  #Return if we were upstream of overlap
+  if($start < $parent_start && $end < $parent_start) {
+    return N x (( $end - $start )+1);
+  }
+  #Return if we were downstream of overlap
+  if($start > $parent_end && $end > $parent_end) {
+    return N x (( $end - $start )+1);
+  }
+  
+  my $prefix  = '';
+  my $suffix = '';
+  my $subslice_start = ($start - $parent_start)+1;
+  my $subslice_end = ($end - $parent_start) + 1;
+  if($start < $parent_start) {
+    $prefix = N x ($parent_start - $start);
+    $subslice_start = 1;
+  }
+  if($end > $parent_end) {
+    $suffix = N x ($end - $parent_end);
+    $subslice_end = (($parent_end - $parent_start)+1);
+  }
+  
+  my $subseq = $parent_slice->subseq($subslice_start, $subslice_end, $strand);
+  
+  return $prefix . $subseq . $suffix;
+}
+
+=head2 subseq()
+  
+  Arg [1]     : Int; start position of the subslice
+  Arg [2]     : Int; end position of the subslice
+  Arg [3]     : Int; strand of the subslice  
+  Example     : my $subseq = $slice->subseq(1, 1_000_000);
+  Description : Returns a portion of the sequence padded with N's if required 
+  Returntype  : Scalar string
+  Exceptions  : None 
+  Caller      : public
+  Status      : -
+
+=cut
+
+sub sub_Slice {
+  die "Unsupported";
+}
+
+
+=head2 __resolver()
+
+  Description : Delegates all non-overriden actions onto the backing slice 
+  Returntype  : CodeRef
+  Exceptions  : None 
+  Caller      : public
+  Status      : -
+
+=cut
+
+sub __resolver {
+  my ($self, $package_name, $method) = @_;
+  return sub {
+    my ($local_self, @args) = @_;
+    return $local_self->__proxy()->$method(@args);
+  };
+}
+
+
+1;