按分隔符读取表格，然后按R中的固定宽度读取 [英] Read table by delimiter then by fixed width in R

问题描述

我有一个制表符分隔的文件，如下所示：

I have a tab-delimited file like this:

RS1->2001 HAPLO1 AAACAAGGAGGAGAAGGAAA ...
RS1->2001 HAPLO2 CAACAAAGAGGAGAAGGAAA ...
RS1->2002 HAPLO1 AAAAAAGGAGGAAAAGGAAA ...
RS1->20020 HAPLO2 CAACAAGGAGGAAGCAGAGC ...
RS1->20021 HAPLO2 CAACAAGGAGGAAGCAGAGC ...

在R中我们可以轻松阅读这三列，我的问题是我需要分开第3列字符。最终结果应该是这样的：

In R we can easily read in these three columns, my problem is that I need separate the 3rd column character by character. The end result should be something like this:

RS1->2001 HAPLO1 A A A C  ...
RS1->2001 HAPLO2 C A A C  ...
RS1->2002 HAPLO1 A A A A  ...
RS1->20020 HAPLO2 C A A C  ...
RS1->20021 HAPLO2 C A A C  ...

我可以先读取3列，然后将第3列的每个条目拆分成字符，但是这个很烦人，我非常希望从一开始就把它弄好。

I can first read the 3 columns in, then split each entry of the 3rd column into characters, but this is annoying, I would very much prefer to get it right from the start.

如果前两列没有出现，我可以用

If the first two columns does not existe, I can achieve the goal with

read.fwf('test.csv', widths=rep(1, 300))

我在想是否可以使用制表符分隔符读取前两列，然后按固定宽度读取第3列。

I am thinking whether I can read in the first 2 columns in by using the tab delimiter and then read the 3rd column by fixed width.

推荐答案

我想到的两个主要选项是 strsplit （如评论中所述）并在@ Ricardo的回答中）和 read.fwf 。 read.fwf 将无法直接处理您的数据，但如果您使用，它可以处理已读入的数据列textConnection（） function。

The two main options that come to mind are strsplit (as mentioned in the comments and in @Ricardo's answer) and read.fwf. read.fwf won't work directly with your data, but it can work on a column of data that has already been read in if you use the textConnection() function.

以下是一个基本示例：

## Create a tab-separated file named "test.txt" in your working directory
cat("2001\tHAPLO1\tAAACAAGGAGGAGAAGGAAA\n",
    "2001\tHAPLO2\tCAACAAAGAGGAGAAGGAAA\n",
    "2002\tHAPLO1\tAAAAAAGGAGGAAAAGGAAA\n",
    "20020\tHAPLO2\tCAACAAGGAGGAAGCAGAGC\n",
    "20021\tHAPLO2\tCAACAAGGAGGAAGCAGAGC\n", 
    file = "test.txt")

## Read it in with `read.delim`
mydata <- read.delim("test.txt", header = FALSE, stringsAsFactors = FALSE)

## Use `read.fwf` on the third column
## Replace "widths" with whatever the maximum width is for that column
## If max width is not known, you can use something like
##    `widths = rep(1, max(nchar(mydata$V3)))`
cbind(mydata[-3], 
      read.fwf(file = textConnection(mydata$V3), widths = rep(1, 20)))
#      V1     V2 V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11 V12 V13 V14 V15 V16 V17 V18 V19 V20
# 1  2001 HAPLO1  A  A  A  C  A  A  G  G  A   G   G   A   G   A   A   G   G   A   A   A
# 2  2001 HAPLO2  C  A  A  C  A  A  A  G  A   G   G   A   G   A   A   G   G   A   A   A
# 3  2002 HAPLO1  A  A  A  A  A  A  G  G  A   G   G   A   A   A   A   G   G   A   A   A
# 4 20020 HAPLO2  C  A  A  C  A  A  G  G  A   G   G   A   A   G   C   A   G   A   G   C
# 5 20021 HAPLO2  C  A  A  C  A  A  G  G  A   G   G   A   A   G   C   A   G   A   G   C

注意：如果您没有使用 stringsAsFactors = FALSE ，则必须更改文件参数：

Note: If you did not use stringsAsFactors = FALSE, you would have to change your file argument to:

file = textConnection(as.character(mydata$V3))

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