LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

     http://www.apache.org/licenses/LICENSE-2.0

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NAME

Bio::EnsEMBL::Utils::PolyA

SYNOPSIS

  my $seq;    # a Bio::Seq object
  my $polyA = Bio::EnsEMBL::Utils::PolyA->new();

  # returns a new Bio::Seq object with the trimmed sequence
  my $trimmed_seq = $polyA->clip($seq);

  # cat put Ns in the place of the polyA/polyT tail
  my $masked_seq = $polyA->mask($seq);

  # can put in lower case the polyA/polyT using any flag:
  my $softmasked_seq = $poly->mask( $seq, 'soft' );

DESCRIPTION

  It reads a Bio::Seq object, it first finds out whether it has a
  polyA or a polyT and then performs one operation in the seq string:
  clipping, masking or softmasking.  It then returns a new Bio::Seq
  object with the new sequence.

METHODS

new