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. `FastqSamplerList` is a list of `FastqSampler` elements.

`FastqStreamer` draws successive subsets from a fastq file, a short illustration is in the example below. `FastqStreamerList` is a list of `FastqStreamer` elements.

### Usage

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

    ## FastqSampler and FastqStreamer
    FastqSampler(con, n=1e6, readerBlockSize=1e8, verbose=FALSE,
        ordered = FALSE)
    FastqSamplerList(..., n=1e6, readerBlockSize=1e8, verbose=FALSE,
        ordered = FALSE)
    FastqStreamer(con, n, readerBlockSize=1e8, verbose=FALSE)
    FastqStreamerList(..., n, 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` | For `FastqSampler`, the size of the sample (number of records) to be drawn. For `FastqStreamer` a `numeric(1)` (set to 1e6 when `n` is missing) providing the number of successive records to be returned on each yield, or an `IRanges`-class delimiting the (1-based) indicies of records returned by each yield; entries in `n` must have non-zero width and must not overlap.
`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.
`ordered` | logical(1) indicating whether sampled reads should be returned in the same order as they were encountered in the file.
`x` | An instance from the `FastqSampler` or `FastqStreamer` class.
`...` | Additional arguments. For `FastqFileList`, `FastqSamplerList`, or `FastqStreamerList`, this can either be a single character vector of paths to fastq files, or several instances of the corresponding `FastqFile`, `FastqSampler`, or `FastqStreamer` objects.
`pattern` | Ignored.
`class` | For developer use, to specify the underlying class contained in the `FastqFileList`.

### 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"`.

`countFastq,FastqFile-method`:

  see also `?countFastq`.

`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.

### Note

`FastqSampler` and `FastqStreamer` use OpenMP threads (when available) during creation of the return value. This may sometimes create problems when a process is already running on multiple threads, e.g., with an error message like

        libgomp: Thread creation failed: Resource temporarily unavailable

A solution is to precede problematic code with the following code snippet, to disable threading

        nthreads <- .Call(ShortRead:::.set_omp_threads, 1L)
        on.exit(.Call(ShortRead:::.set_omp_threads, nthreads))

### See Also

`readFastq`, `writeFastq`, `countFastq`, `yield`.

### Examples

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

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

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

    ## Return sample as ordered in original file
    f <- FastqSampler(fl, 50, ordered=TRUE)
    yield(f)
    close(f)

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

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

    ## iterating over IRanges
    rng <- IRanges(c(50, 100, 200), width=10:8)
    f <- FastqStreamer(fl, rng)
    while (length(fq <- yield(f))) {
        print(length(fq))
    }
    close(f)

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

[Package ShortRead version 1.52.0 Index]