Bio::EnsEMBL::Utils::Sequence Class Reference

Public Member Functions
public void	reverse_comp ()
public void	expand ()

Detailed Description

Synopsis

use Bio::EnsEMBL::Utils::Sequence qw(reverse_comp expand);
 
my $seq = 'ACTTTAAAGGCTATCCCAATATG';
 
print "my sequence = $seq\n";
 
reverse_comp( \$seq );
 
print "my reverse comp = $seq\n";
 
my $compressed_seq = '(AC)3';
 
print "my expanded seq is = expand($compressed_seq)";

Definition at line 22 of file Sequence.pm.

Member Function Documentation

expand()

public void Bio::EnsEMBL::Utils::Sequence::expand

(

)

  Arg [1]    : reference to a string $seqref
  Example    :

 use Bio::EnsEMBL::Utils::Sequence qw(expand);
@verbatim
         $seq = '(AC)3';
         expand(\$seq);
         print $seq;
@endverbatim

  Description: Expands a genomic sequence. The string is passed by reference
               rather than by value for memory efficiency.
  Returntype : none
  Exceptions : none
  Caller     : SequenceAdaptor, SliceAdaptor

Code:

reverse_comp()

public void Bio::EnsEMBL::Utils::Sequence::reverse_comp

(

)

  Arg [1]    : reference to a string $seqref
  Example    :

 use Bio::EnsEMBL::Utils::Sequence qw(reverse_comp);
@verbatim
         $seq = 'ACCTGAA';
         reverse_comp(\$seq);
         print $seq;
@endverbatim

  Description: Does an in place reverse compliment of a passed in string
               reference.  The string is passed by reference
               rather than by value for memory efficiency.
  Returntype : none
  Exceptions : none
  Caller     : SequenceAdaptor, SliceAdaptor

Code:

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The documentation for this class was generated from the following file:

• ensembl/modules/Bio/EnsEMBL/Utils/Sequence.pm