BioRead

Contain sequence reads and their quality data

Description

The BioRead object contains sequencing read data, including sequence headers, nucleotide sequences, and quality scores.

Create a BioRead object from NGS (next-generation sequencing) data stored in an FASTQ- or SAM-formatted file. Each element in the object has a sequence, header, and quality score associated with it. Use the object properties and functions to explore, access, filter, and manipulate all the data or a subset of the data. If you have data with reads that are already mapped to a reference sequence, and you need to access alignment records, use BioMap instead.

Creation

Syntax

bioreadObj = BioRead

bioreadObj = BioRead(File)

bioreadObj = BioRead(S)

bioreadObj = BioRead(Seqs)

bioreadObj = BioRead(Seqs,Quals)

bioreadObj = BioRead(Seqs,Quals,Headers)

bioreadObj = BioRead(___,Name,Value)

Description

bioreadObj = BioRead creates an empty BioRead object bioreadObj.

bioreadObj = BioRead(File) creates a BioRead object from File, an FASTQ- or SAM-formatted file. The data remains in the source file after the object is created, and you have access to data through the object properties but cannot modify the properties, except the Name property.

bioreadObj = BioRead(S) creates a BioRead object from S, a MATLAB^® structure, containing the fields Header, Sequence, and Quality. The data from S remains in memory, and you can modify the properties of the object.

bioreadObj = BioRead(Seqs) creates a BioRead object from Seqs, a cell array of character vectors or string vector containing nucleotide sequences.

bioreadObj = BioRead(Seqs,Quals) creates a BioRead object from Seqs and sets the Quality property of the object to Quals, a cell array of character vectors or string vector containing the ASCII representation of per-base quality scores for each read.

bioreadObj = BioRead(Seqs,Quals,Headers) also sets the Header property of the object to Headers, a cell array of character vectors or string vector containing the header text for each read.

bioreadObj = BioRead(___,Name,Value) specifies options using one or more name-value pair arguments in addition to input arguments in previous syntaxes. For instance, br = BioRead('SRR005164_1_50.fastq','InMemory',true) specifies to load the data in memory instead of leaving it in the source file.

Input Arguments

File — Name of FASTQ- or SAM-formatted file

character vector | string

Name of FASTQ- or SAM-formatted file, specified as a character vector or string.

The BioRead object accesses data using an auxiliary index file. The index file must have the same name as the source file, but with an .idx extension. If the index file is not in the same folder as the source file, the BioRead function creates the index file in that folder.

Note

Because the data remains in the source file, do not delete the source file and auxiliary index file.

Example: 'ex1.sam'

Data Types: char

S — Sequence information

structure

Sequence information, specified as a structure. S must contain the fields Header, Sequence, and Quality. For instance, the fastqread and samread functions return such a structure.

Example: S

Data Types: struct

Seqs — Nucleotide sequences

cell array of character vectors | string vector

Nucleotide sequences, specified as a cell array of character vectors or string vector.

Data Types: cell

Quals — Sequence quality information

cell array of character vectors | string vector

Sequence quality information, specified as a cell array of character vectors.

Data Types: cell

Name-Value Arguments

Specify optional pairs of arguments as Name1=Value1,...,NameN=ValueN, where Name is the argument name and Value is the corresponding value. Name-value arguments must appear after other arguments, but the order of the pairs does not matter.

Before R2021a, use commas to separate each name and value, and enclose Name in quotes.

Example: br = BioRead('SRR005164_1_50.fastq','InMemory',true) specifies to load the data in memory instead of leaving it in the source file.

InMemory — Boolean indicator to keep data in memory

false (default) | true

Boolean indicator to keep data in memory, specified as the comma-separated pair consisting of 'InMemory' and true or false.

When you create a BioRead object from a file, the object does not load the data in memory, but leaves it in the source file and accesses it using an index file to make the process more memory efficient. You cannot modify the object properties if you do not load the data in memory.

If the first input is not a file, this name-value pair argument is ignored, and the data is automatically placed in memory.

Example: 'InMemory',true

Data Types: logical

IndexDir — Path to index file folder

character vector | string

Path to the index file folder where the index file exists or is created, specified as the comma-separated pair consisting of 'IndexDir' and a character vector or string.

Example: 'IndexDir','C:\data\'

Data Types: char

Properties

Header — Header information of reads

cell array of character vectors

Header information of reads, specified as a cell array of character vectors. Each character vector represents the header text for each read. There is a one-to-one relationship between the number and order of character vectors (elements) in the Header and Sequence properties, unless Header is an empty cell array.

Data Types: cell

Name — Object name

character vector | string

Object name, specified as a character vector or string.

Example: 'seqdata'

Data Types: char

NSeqs — Number of reads

positive integer

Number of reads in the object, specified as a positive integer.

Example: 20000

Data Types: double

Quality — Per-base quality scores for all reads

cell array of character vectors

Per-base quality scores for all reads, specified as a cell array of character vectors. Each element is an ASCII representation of per-base quality scores for each read. A one-to-one relationship exists between the number and order of elements in Quality and Sequence, unless Quality is an empty cell array.

Example: {'<<:<<<','<<<7<:'}

Data Types: cell

Sequence — Nucleotide sequences

cell array of character vectors

Nucleotide sequences (reads), specified as a cell array of character vectors.

Example: {'TATCTG','ATCTAC'}

Data Types: cell

Object Functions

combine	Combine two objects
get	Retrieve property of object
getHeader	Retrieve sequence headers from object
getQuality	Retrieve sequence quality information from object
getSequence	Retrieve sequences from object
getSubsequence	Retrieve partial sequences from object
getSubset	Retrieve subset of elements from object
set	Set property of object
setHeader	Update header information of reads
setQuality	Update quality information
setSequence	Update read sequences
setSubsequence	Update partial sequences
setSubset	Update elements of object
write	Write contents of BioRead or BioMap object to file

Examples

Create BioRead Object from NGS Data

Create a BioRead object from sequencing read data saved in a FASTQ-formatted file.

br = BioRead('SRR005164_1_50.fastq')

br = 
  BioRead with properties:

     Quality: [50x1 File indexed property]
    Sequence: [50x1 File indexed property]
      Header: [50x1 File indexed property]
       NSeqs: 50
        Name: ''

By default, when creating a BioRead object from a file, the function also creates an index file if one does not already exist. This example uses an existing index file created and saved in:

fullfile(matlabroot,'toolbox','bioinfo','bioinfodata','SRR005164_1_50.fastq.idx')

The data remains in the source file, and the object accesses the data using the index file, making the process more memory efficient. But you cannot edit the object properties, except the Name property.

To edit the properties, set 'InMemory' to true.

brEdit = BioRead('SRR005164_1_50.fastq','InMemory',true);
brEdit.Header(1) = {'SR1'};

brEdit.Header(1)

ans = 1×1 cell array
    {'SR1'}

If you create the object from a MATLAB structure or cell array of nucleotide sequences, the sequence data is always saved in memory by default, and the InMemory option is ignored.

For instance, generate MATLAB variables containing synthetic sequences and quality scores.

seqs = {randseq(10);randseq(15);randseq(20)};
quals = {repmat('!',1,10); repmat('%',1,15);repmat('&',1,20)};
headers = {'H1';'H2';'H3'};

Create a structure using these variables.

structData = struct('Header',headers,'Sequence',seqs,'Quality',quals);

Create a BioRead object from the structure.

brStruct = BioRead(structData);

You can edit the properties of the object because the data remains in memory.

brStruct.Header(1) = {'H1.1'};
brStruct.Header(1)

ans = 1×1 cell array
    {'H1.1'}

Version History

Introduced in R2010a