虽然读线，与多个分隔符awk的$行 [英] While read line, awk $line with multiple delimiters

问题描述

我想这，除了要告诉awk的是， ：或制表\\ t时文件的定界符基于所述第五字段可以是一个冒号进行分割。我做的的awk -F'[：\\ t]'。单独部分，它确实打印正确的$ 5外地

I am trying a small variation of this, except I telling awk that the delimiter of the file to be split based on the 5th field can either be a colon ":" or a tab \t. I do the awk -F '[:\t]' part alone, it does indeed print the right $5 field.

然而，当我试图将其纳入更大的命令这一点，它返回以下错误：

However, when I try to incorporate this into the bigger command, it returns the following error:

                                                             print > f
awk: cmd. line:9:                                            ^ syntax error

这是code：

awk -F '[:\t]' '    # read the list of numbers in Tile_Number_List
    FNR == NR {
        num[$1]
        next
    }

    # process each line of the .BAM file
    # any lines with an "unknown" $5 will be ignored
    $5 in num {
        f = "Alignments_" $5 ".sam"        print > f
    } ' Tile_Number_List.txt little.sam

为什么不将它与-F选项工作？

Why won't it work with the -F option?

推荐答案

这个问题是不是与 FS 的值，它是这条线由错误指向：

The problem isn't with the value of FS it's this line as pointed to by the error:

f = "Alignments_" $5 ".sam"        print > f

您有一条线两条语句所以无论他们分离出; 或换行符：

You have two statements on one line so either separate them with a ; or a newline:

f = "Alignments_" $5 ".sam"; print > f

或者

f = "Alignments_" $5 ".sam"
print > f

---

由于采用全单行：

---

As full one liner:

awk -F '[:\t]' 'FNR==NR{n[$1];next}$5 in n{print > ("Alignments_"$5".sam")}'

或者作为一个脚本文件，即 script.awk ：

BEGIN {
    FS="[:\t]" 
}
# read the list of numbers in Tile_Number_List
FNR == NR {
    num[$1]
    next
}
# process each line of the .BAM file
# any lines with an "unknown" $5 will be ignored
$5 in num {
    f = "Alignments_" $5 ".sam"        
    print > f
}

要以这种形式运行的awk -f script.awk Tile_Number_List.txt little.sam 。

编辑：

字符 - 用于从标准输入，而不是一个文件有许多的* nix工具重新present输入。

The character - is used to represent input from stdin instead of a file with many *nix tools.

command | awk -f script.awk Tile_Number_List.txt -

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