R: Sampling and streaming records from fastq files

FastqFile-class {ShortRead}

R Documentation

Sampling and streaming records from fastq files

Description

FastqFile represents a path and connection to a fastq file. FastqFileList is a list of such connections.

FastqSampler draws a subsample from a fastq file. yield is the method used to extract the sample from the FastqSampler instance; a short illustration is in the example below.

FastqStreamer draws successive subsets from a fastq file. Iterating over the stream will eventually yield the entire file; a short illustration is in the example below.

Usage

## FastqFile and FastqFileList
FastqFile(con, ...)
FastqFileList(...)
## S3 method for class 'ShortReadFile'
open(con, ...)
## S3 method for class 'ShortReadFile'
close(con, ...)
## S4 method for signature 'FastqFile'
readFastq(dirPath, pattern=character(), ...)

## FastqSampler and FastqStreamer
FastqSampler(con, n=1e6, readerBlockSize=1e8, verbose=FALSE)
FastqStreamer(con, n=1e6, readerBlockSize=1e8, verbose=FALSE)
yield(x, ...)

Arguments

`con, dirPath`	A character string naming a connection, or (for `con`) an R connection (e.g., `file`, `gzfile`).
`n`	The size of the sample (number of records) to be drawn.
`readerBlockSize`	The number of bytes or characters to be read at one time; smaller `readerBlockSize` reduces memory requirements but is less efficient.
`verbose`	Display progress.
`x`	An instance from the `FastqSampler` or `FastqStreamer` class.
`...`	Additional arguments. For `FastqFileList`, this can either be a single character vector of paths to fastq files, or several instances of `FastqFile` objects.
`pattern`	Ignored.

Objects from the class

Available classes include:

FastqFile: A file path and connection to a fastq file.
FastqFileList: A list of FastqFile instances.
FastqSampler: Uniformly sample records from a fastq file.
FastqStreamer: Iterate over a fastq file, returning successive parts of the file.

Methods

The following methods are available to users:

readFastq,FastqFile-method:: see also ?readFastq.
writeFastq,ShortReadQ,FastqFile-method:: see also ?writeFastq, ?"writeFastq,ShortReadQ,FastqFile-method".
yield:: Draw a single sample from the instance. Operationally this requires that the underlying data (e.g., file) represented by the Sampler instance be visited; this may be time consuming.

Examples

sp <- SolexaPath(system.file('extdata', package='ShortRead'))
fl <- file.path(analysisPath(sp), "s_1_sequence.txt")

f <- FastqFile(fl)
rfq <- readFastq(f)

f <- FastqSampler(fl, 50)
yield(f)    # sample of size n=50
yield(f)    # independent sample of size 50

f <- FastqStreamer(fl, 50)
yield(f)    # records 1 to 50
yield(f)    # records 51 to 100

## iterating over an entire file
f <- FastqStreamer(fl, 50)
while (length(fq <- yield(f))) {
    ## do work here
    print(length(fq))
}

## Internal fields, methods, and help; for developers
ShortRead:::.FastqSampler_g$methods()
ShortRead:::.FastqSampler_g$fields()
ShortRead:::.FastqSampler_g$help("yield")

[Package ShortRead version 1.12.4 Index]