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write

Write contents of BioRead or BioMap object to file

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Syntax

write(object,fName)
write(object,fName,Name,Value)

Description

write(object,fName) writes the contents of a BioRead or BioMap object to a file named fName.

example

write(object,fName,Name,Value) uses additional options specified by one or more name-value pair arguments. For example, write(object,'data','Format','FASTQ') saves the contents of the object in the FASTQ-formatted file data.fastq.

example

Examples

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Create a BioRead object from an FASTQ file.

BRObj = BioRead('SRR005164_1_50.fastq');

Extract the first 10 elements from BRObj and store them in a new object.

subsetBRObj = getSubset(BRObj, [1:10]);

Write the contents of the subset data to a file named subsetData.fastq in the local C drive. By default, the file is FASTQ-formatted because the object contains the quality data.

write(subsetBRObj, 'C:\subsetData');

Input Arguments

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Object containing the read data, specified as a BioRead or BioMap object.

Example: bioreadObj

Name of the file where the contents of object are written, specified as a character vector or string.

The function adds the file extension automatically depending on the type of data the object contains. If you provide the extension, the function checks for consistency between the extension and the data format of the object. The file name can be prefixed by a file path. If the path is missing, the function writes the file to the same folder where the source file is located or to the current folder if the data is in memory.

Example: 'output'

Data Types: char

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: write(object,'data','Format','FASTQ') saves the contents of the object in the FASTQ-formatted file data.fastq.

File format, specified as a comma-separated pair consisting of 'Format' and a character vector or string.

For BioRead objects, available formats are 'FASTA' and 'FASTQ'. The default format is 'FASTA' if the object does not contain qualities, that is, the Quality property is empty. Otherwise, the default format is 'FASTQ'.

For BioMap objects, available formats are 'FASTA', 'FASTQ', 'SAM', and 'BAM' (default).

Example: 'Format','FASTA'

Data Types: char

Boolean indicator to overwrite an existing file, specified as a comma-separated pair consisting of 'Overwrite' and true or false. If true, the function overwrites the file and deletes any respective index file (*.idx,*.bai,*.linearindex) or ordered file (*.ordered.bam, *.ordered.sam) that is no longer needed.

Example: 'Overwrite',true

Data Types: logical

Version History

Introduced in R2010a

See Also

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