getSequence

Class: BioRead

Retrieve sequences from object

Syntax

Sequences = getSequence(BioObj)
Sequences = getSequence(BioObj, Subset)

Description

Sequences = getSequence(BioObj) returns Sequences, a cell array of strings containing the letter representations of nucleotide sequences from an object.

Sequences = getSequence(BioObj, Subset) returns sequence strings for only object elements specified by Subset.

Input Arguments

BioObj

Object of the BioRead or BioMap class.

Subset

One of the following to specify a subset of the elements in BioObj:

  • Vector of positive integers

  • Logical vector

  • Cell array of strings containing valid sequence headers

    Note:   If you use a cell array of header strings to specify Subset, be aware that a repeated header specifies all elements with that header.

Output Arguments

Sequences

Cell array of strings containing the sequences specified by Subset in BioObj.

Examples

Retrieve the sequences from different elements of a BioRead object:

% Construct a BioRead object from a FASTQ file 
BRObj = BioRead('SRR005164_1_50.fastq');
% Retrieve the sequence of the second element in the object
getSequence(BRObj, 2);
getSequence(BRObj, {'SRR005164.2'});
getSequence(BRObj, [false true false]);
% Retrieve the sequences of the first and third elements in the object
getSequence(BRObj, [1 3]);
getSequence(BRObj, {'SRR005164.1', 'SRR005164.3'});
getSequence(BRObj, [true false true]);
% Retrieve the sequences of all the elements in the object
getSequence(BRObj, 1:50);

Alternatives

An alternative to using the getSequence method is to use dot indexing with the Sequence property:

BioObj.Sequence(Indices)

In the previous syntax, Indices is a vector of positive integers or a logical vector. Indices cannot be a cell array of strings containing sequence headers.

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