Bio::EnsEMBL::DBSQL::FastaSequenceAdaptor Class Reference

Inheritance diagram for Bio::EnsEMBL::DBSQL::FastaSequenceAdaptor:

Public Member Functions
public	new ()
public	fetch_by_Slice_start_end_strand ()
public	faindex ()
public	can_access_Slice ()
public	store ()
protected	_fetch_raw_seq ()
Public Member Functions inherited from Bio::EnsEMBL::DBSQL::BaseSequenceAdaptor
public StringRef	fetch_by_Slice_start_end_strand ()
public Boolean	can_access_Slice ()
public Bio::EnsEMBL::Slice	expand_Slice ()
public Bio::EnsEMBL::DBSQL::SequenceAdaptor	new ()
protected	_init_seq_instance ()
public void	clear_cache ()
public	chunk_power ()
public	cache_size ()
public	seq_cache_max ()
protected ScalarRef	_fetch_raw_seq ()
protected ScalarRef	_fetch_seq ()

Detailed Description

Description

This sequence adaptor extends the BaseSequenceAdaptor code to provide an 
implementation of the .fai index lookup as defined by samtools. The code uses
this indexing system to access portions of sequence and translates Slice requests
into sensible locations for our FASTA query layer.

The adaptor must be initalised with access to a Faidx compatible object and the FASTA
file backing must use the same seq_region_name as the querying slices otherwise
we cannot return the required data.

Definition at line 20 of file FastaSequenceAdaptor.pm.

Member Function Documentation

_fetch_raw_seq()

protected Bio::EnsEMBL::DBSQL::FastaSequenceAdaptor::_fetch_raw_seq

(

)

  Description : Provides access to the underlying faindex object and returns a sequence scalar ref

Code:

can_access_Slice()

public Bio::EnsEMBL::DBSQL::FastaSequenceAdaptor::can_access_Slice

(

)

  Description : Checks the lookup to see if we have access to the Slice given (using 
                seq region name as the ID). We reject any Circular Slice

Code:

faindex()

public Bio::EnsEMBL::DBSQL::FastaSequenceAdaptor::faindex

(

)

  Description : Holds a reference to the Faindex object to use for sequence access

Code:

fetch_by_Slice_start_end_strand()

public Bio::EnsEMBL::DBSQL::FastaSequenceAdaptor::fetch_by_Slice_start_end_strand

(

)

  
  Arg [1]     : Bio::EnsEMBL::Slice; $slice. Slice to fetch sequence for
  Arg [2]     : Integer; $start. Start of region to retrieve relative to the Slice (defaults to 1)
  Arg [3]     : Integer; $end. End of region to retreive relative to the Slice (defaults to length)
  Arg [4]     : Integer; $strand. Strand to fetch (defaults to 1)
  Description : Fetches sequence for the given slice. Unlike the normal SequenceAdaptor we assume
                Sequence is held in a FASTA file under the Slice's seq_region_name.
  Exception   : Thrown if we are given a circular slice
 

Code:

new()

public Bio::EnsEMBL::DBSQL::FastaSequenceAdaptor::new

(

)

  
  Arg [1]     : FileFaidx; $faindex. A FileFaidx object or a compatible version
  Arg [2]     : Integer; $chunk_power. Size of the region to cache
  Arg [3]     : Integer; $cache_size. Number of regions to cache
  Description : Builds an instance of the FastaSequenceAdaptor

Code:

store()

public Bio::EnsEMBL::DBSQL::FastaSequenceAdaptor::store

(

)

  
  Description : Unsupported operation. Please use a FASTA serialiser

Code:

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

• ensembl/modules/Bio/EnsEMBL/DBSQL/FastaSequenceAdaptor.pm