Bio::EnsEMBL::Utils Sequence
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Summary
Bio::EnsEMBL::Utils::Sequence - Utility functions for sequences
Package variables
No package variables defined.
Included modules
Exporter
Inherit
Exporter
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)";
Description
No description!
Methods
expandDescriptionCode
reverse_compDescriptionCode
Methods description
expandcode    nextTop
  Arg [1]    : reference to a string $seqref
Example : use Bio::EnsEMBL::Utils::Sequence qw(expand);
$seq = '(AC)3'; expand(\$seq); print $seq; 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
reverse_compcodeprevnextTop
  Arg [1]    : reference to a string $seqref
Example : use Bio::EnsEMBL::Utils::Sequence qw(reverse_comp);
$seq = 'ACCTGAA'; reverse_comp(\$seq); print $seq; 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
Methods code
expanddescriptionprevnextTop
sub expand {
  my $seq_ref = shift;
     $$seq_ref =~ s/(\w*)\((\w+)\)(\d+)/$1.$2 x $3/eg  if ($$seq_ref =~ /\(/);#expressions with parenthesis, expand the alleles			    
return; } 1;
}
reverse_compdescriptionprevnextTop
sub reverse_comp {
  my $seqref = shift;

  $$seqref = reverse( $$seqref );
  $$seqref =~
    tr/acgtrymkswhbvdnxACGTRYMKSWHBVDNX/tgcayrkmswdvbhnxTGCAYRKMSWDVBHNX/;

  return;
}
General documentation
LICENSETop
  Copyright (c) 1999-2009 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 /info/about/code_licence.html
CONTACTTop
  Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at <helpdesk@ensembl.org>.