FastqFile-class(ShortRead)
FastqFile-class()所属R语言包：ShortRead
Sampling and streaming records from fastq files
采样和流fastq文件记录
译者：生物统计家园网 机器人LoveR
描述----------Description----------
FastqFile represents a path and connection to a fastq file. FastqFileList is a list of such connections.
FastqFile代表到fastq文件的路径和连接。 FastqFileList是一个这样的连接列表。
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.
FastqSampler绘制一个从fastq文件的子样本。 yield是FastqSampler实例提取样品使用的方法，在下面的例子是一个简短的插图。
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.
FastqStreamer投篮连续从fastq文件的子集。迭代流，最终将产生整个文件，在下面的例子是一个简短的插图。
用法----------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, ...)
参数----------Arguments----------
参数：con, dirPath
A character string naming a connection, or (for con) an R connection (e.g., file, gzfile).
一个字符串，命名连接，或（con）的R连接（例如，file，gzfile）。
参数：n
The size of the sample (number of records) to be drawn.
要绘制的样本大小（记录数）。
参数：readerBlockSize
The number of bytes or characters to be read at one time; smaller readerBlockSize reduces memory requirements but is less efficient.
字节或字符数要读一次;小readerBlockSize降低内存需求，但效率较低。
参数：verbose
Display progress.
显示进度。
参数：x
An instance from the FastqSampler or FastqStreamer class.
FastqSampler或FastqStreamer类的实例。
参数：...
Additional arguments. For FastqFileList, this can either be a single character vector of paths to fastq files, or several instances of FastqFile objects.
额外的参数。 FastqFileList，这可以是一个单个字符fastq文件，或FastqFile对象的多个实例的路径向量。
参数：pattern
Ignored.
忽略。
类的对象----------Objects from the class----------
Available classes include:
可用的类别包括：
FastqFile A file path and connection to a fastq file.
FastqFile文件路径和连接到fastq文件。
FastqFileList A list of FastqFile instances.
FastqFileList的FastqFile实例列表。
FastqSampler Uniformly sample records from a fastq
FastqSampler一致样品从fastq记录
FastqStreamer Iterate over a fastq file, returning
FastqStreamer迭代超过fastq文件的，返回
方法----------Methods----------
The following methods are available to users:
用户可用下列方法：
readFastq,FastqFile-method: see also
readFastq,FastqFile-method：又见
writeFastq,ShortReadQ,FastqFile-method: see also ?writeFastq,
writeFastq,ShortReadQ,FastqFile-method：又见?writeFastq
yield: Draw a single sample from the instance. Operationally this requires that the underlying data (e.g., file) represented by the Sampler instance be
yield从实例：绘制单一样本。运作，这要求Sampler实例为代表的底层数据（例如，文件）
参见----------See Also----------
readFastq, writeFastq, yield.
readFastq，writeFastq，yield。
举例----------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[样本大小n = 50]
yield(f) # independent sample of size 50[独立样本的大小50]
f <- FastqStreamer(fl, 50)
yield(f) # records 1 to 50[记录1到50]
yield(f) # records 51 to 100[记录51到100]
## iterating over an entire file[＃遍历整个文件]
f <- FastqStreamer(fl, 50)
while (length(fq <- yield(f))) {
## do work here[＃在这里工作]
print(length(fq))
}
## Internal fields, methods, and help; for developers[＃内部字段，方法，并帮助开发人员]
ShortRead:::.FastqSampler_g$methods()
ShortRead:::.FastqSampler_g$fields()
ShortRead:::.FastqSampler_g$help("yield")
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注：
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发表于 2012-2-26 14:04:29
