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Bio::EnsEMBL::Utils::PolyA Class Reference
Inheritance diagram for Bio::EnsEMBL::Utils::PolyA:

List of all members.


Class Summary

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.
 

Definition at line 30 of file PolyA.pm.

Available Methods

protected _clip ()
protected _find_polyA ()
protected _mask ()
protected _rearrange ()
protected _softmask ()
public clip ()
public has_polyA_track ()
public mask ()
public new ()
public stack_trace ()
public stack_trace_dump ()
public throw ()
public verbose ()
public warn ()

Method Documentation

protected Bio::EnsEMBL::Utils::PolyA::_clip ( )

Undocumented method

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protected Bio::EnsEMBL::Utils::PolyA::_find_polyA ( )

Undocumented method

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protected Bio::EnsEMBL::Utils::PolyA::_mask ( )

Undocumented method

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protected Bio::EnsEMBL::Root::_rearrange ( ) [inherited]
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protected Bio::EnsEMBL::Utils::PolyA::_softmask ( )

Undocumented method

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public Bio::EnsEMBL::Utils::PolyA::clip ( )

Undocumented method

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public Bio::EnsEMBL::Utils::PolyA::has_polyA_track ( )

Undocumented method

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public Bio::EnsEMBL::Utils::PolyA::mask ( )

Undocumented method

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public Bio::EnsEMBL::Utils::PolyA::new ( )
 
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Reimplemented from Bio::EnsEMBL::Root.

public Bio::EnsEMBL::Root::stack_trace ( ) [inherited]
Deprecated:
 
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public Bio::EnsEMBL::Root::stack_trace_dump ( ) [inherited]
Deprecated:
 
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public Bio::EnsEMBL::Root::throw ( ) [inherited]
Deprecated:
 
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public Bio::EnsEMBL::Root::verbose ( ) [inherited]
Deprecated:
 
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public Bio::EnsEMBL::Root::warn ( ) [inherited]
Deprecated:
 
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The documentation for this class was generated from the following file: