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

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NAME

Bio::EnsEMBL::DBSQL::FastaSequenceAdaptor

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.

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

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

faindex

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

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

store

Description : Unsupported operation. Please use a FASTA serialiser

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