Sampling and streaming records from fastq files
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.
## 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, ...)con, dirPath |
A character string naming a connection, or (for
|
n |
For |
readerBlockSize |
The number of bytes or characters to be read at
one time; smaller |
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 |
... |
Additional arguments. For |
pattern |
Ignored. |
class |
For developer use, to specify the underlying class
contained in the |
Available classes include:
FastqFileA file path and connection to a fastq file.
FastqFileListA list of FastqFile instances.
FastqSamplerUniformly sample records from a fastq file.
FastqStreamerIterate over a fastq file, returning successive parts of the file.
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.
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))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")Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.