readFasta(ShortRead)
readFasta()所属R语言包：ShortRead
Read and write FASTA files to or from ShortRead objects
读取和写入FASTA格式的文件或从ShortRead对象
译者：生物统计家园网 机器人LoveR
描述----------Description----------
readFasta reads all FASTa-formated files in a directory dirPath whose file name matches pattern pattern, returning a compact internal representation of the sequences and quality scores in the files. Methods read all files into a single R object; a typical use is to restrict input to a single FASTQ file.
readFasta读取目录dirPath的文件名匹配模式的所有FASTA格式文件pattern，返回一个紧凑的内部文件中的序列和质量分数表示。方法读取所有文件到一个单一的R对象，是一个典型的使用，以限制输入一个单一FASTQ文件。
writeFasta writes an object to a single file, using mode="w" (the default) to create a new file or mode="a" append to an existing file. Attempting to write to an existing file with mode="w" results in an error.
writeFasta写了一个对象，一个单一的file“使用mode="w"（默认），以创建一个新文件或mode="a"追加到现有的文件。试图写入到一个现有的文件mode="w"在一个错误的结果。
用法----------Usage----------
readFasta(dirPath, pattern = character(0), ...,
nrec=-1L, skip=0L)
## S4 method for signature 'character'
readFasta(dirPath, pattern = character(0), ...,
nrec=-1L, skip=0L)
writeFasta(object, file, mode="w", ...)
## S4 method for signature 'DNAStringSet'
writeFasta(object, file, mode="w", ...)
参数----------Arguments----------
参数：dirPath
A character vector giving the directory path (relative or absolute) or single file name of FASTA files to be read.
字符向量的目录路径（相对或绝对）或FASTA格式的文件要读取单个文件名。
参数：pattern
The (grep-style) pattern describing file names to be read. The default (character(0)) results in (attempted) input of all files in the directory.
（grep式）模式描述被读取的文件名。默认（character(0)）（未遂）输入目录中的所有文件中的结果。
参数：object
An object to be output in fasta format.
对象是fasta格式的输出。
参数：file
A length 1 character vector providing a path to a file to the object is to be written to.
被写入到一个文件对象提供了一个路径一个长度为1的特征向量。
参数：mode
A length 1 character vector equal to either "w" or "a" to write to a new file or append to an existing file, respectively.
一个长度为1的特征向量等于或者W或一写一个新的文件或追加到现有文件，分别为。
参数：...
Additional arguments used by methods or, for writeFasta, write.XStringSet.
额外的参数，采用的方法，writeFasta，write.XStringSet。
参数：nrec
See ?read.DNAStringSet.
看到?read.DNAStringSet。
参数：skip
See ?read.DNAStringSet.
看到?read.DNAStringSet。
值----------Value----------
readFasta returns a DNAStringSet. containing sequences and qualities contained in all files in dirPath matching pattern. There is no guarantee of order in which files are read.
readFasta返回一个DNAStringSet。包含序列，并在所有文件中包含dirPath匹配pattern素质。有没有为了保证文件是只读的。
writeFasta is invoked primarily for its side effect, creating or appending to file file. The function returns, invisibly, the length of object, and hence the number of records written. There is a writeFasta method for any class derived from ShortRead.
writeFasta被调用，主要用于其副作用，创建或追加到文件file。函数返回时，无形中，object的长度，因此书面记录。还有writeFastaShortRead派生的任何类的方法。
作者（S）----------Author(s)----------
Martin Morgan
举例----------Examples----------
showMethods("readFasta")
showMethods("writeFasta")
f1 <- system.file("extdata", "someORF.fa", package="Biostrings")
rfa <- readFasta(f1)
sread(rfa)
id(rfa)
sp <- SolexaPath(system.file('extdata', package='ShortRead'))
rfq <- readFastq(analysisPath(sp), pattern="s_1_sequence.txt")
file <- tempfile()
writeFasta(rfq, file)
readLines(file, 8)
writeFasta(sread(rfq), file) # no 'id's [没有“身份证]
转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。
注：
注1：为了方便大家学习，本文档为生物统计家园网机器人LoveR翻译而成，仅供个人R语言学习参考使用，生物统计家园保留版权。
注2：由于是机器人自动翻译，难免有不准确之处，使用时仔细对照中、英文内容进行反复理解，可以帮助R语言的学习。
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发表于 2012-2-26 14:05:49
