虽然读线，AWK $线 [英] While read line, awk $line

问题描述

我有一个包含数字的列表的文件。我有不同的条目和几个字段每个第二个文件。

I have a file that contains a list of numbers. I have a second file with various entries and several fields each.

我想要做的是让他们的第12场等于1号的所有行，并将其放置在一个新的文件，然后到第二个号码，依此类推。

What I want to do is to get all the lines whose 12th field is equal to the 1st number and place them in a new file, then to the second number, and so on.

我写了一个班轮是有道理的，但我不明白，为什么它不会工作。

I wrote a one-liner that makes sense, but I can't figure out why it won't work.

这是一个数字的列表：

猫 truncations_list.txt

3
318
407
412
7

与要排序的条目的文件是：

The file with the entries to be sorted is:

M00970:45:000000000-A42FD:1:1101:14736:1399 TGCCCAGTGCTCTGAATGTNNNNNTGAAGAAATTCAAGTAAGCGCGGGTCATCGGCNGGAGTAACTATGACTCTNTTAAGGAGGACCAATATGAACCANACNNNNNNNNNACTNTATCTAGGGTTCCCTGCACAGTATGTGNCC    79  TGCCCAGTGCTCTGAATGTNNNNNTGAAGAAATTCAAGTAAGCGCGGGTCATCGGCNGGAGTAACTATGACTCTNTTAA 65  GGAGGACCAATATGAACCANACNNNNNNNNNACTNTATCTAGGGTTCCCTGCACAGTATGTGNCC   79S65M  1   81  TGCCCAGTGCTCTGAATGTNNNNNTGAAGAAATTCAAGTAAGCGCGGGTCATCGGCNGGAGTAACTATGACTCTNTTAAGG   -2  318
M00970:45:000000000-A42FD:1:1101:15371:1399 TGCCCAGTGCTCTGAATGTNNNNNTGAAGAAATTCAAGTAAGCGCGGGTCAACGGCNGGAGTAACTATGACTCTNTTAAGGAGTCGGTGTTCACATGCNATNNNNNNNNNCAGNCGAACTTGATGAAGAACGTCGACGTGTNGG    83  TGCCCAGTGCTCTGAATGTNNNNNTGAAGAAATTCAAGTAAGCGCGGGTCAACGGCNGGAGTAACTATGACTCTNTTAAGGAG 61  TCGGTGTTCACATGCNATNNNNNNNNNCAGNCGAACTTGATGAAGAACGTCGACGTGTNGG   83S61M  1   81  TGCCCAGTGCTCTGAATGTNNNNNTGAAGAAATTCAAGTAAGCGCGGGTCAACGGCNGGAGTAACTATGACTCTNTTAAGG   2   407

这是我的命令：

file="truncations_list.txt"
while read line; do awk '$12==$line' R2_Output.txt >reads_$line.txt ; done <"$file"

此命令将创建的所有文件reads_412.txt等，但所有的文件都是空的。

This command will create all the files "reads_412.txt", etc, but all the files are empty.

我AP preciate您的帮助！

I appreciate your help!

推荐答案

您主要问题是，awk程序是用单引号，因此，$线变量是永远不会扩大。快速修复

Your main problem is that the awk program is in single quotes, so the "$line" variable is never expanded. The quick fix is

awk -v num=$line '$12==num' R2_Output.txt

不过，不这样做。您正在阅读的输出文件，一旦在数字文件中的每一行。你可以把它只需通过每个文件只有一个时间阅读工作：

But, don't do that. You're reading the output file once for each line in the numbers file. You can make it work by just reading through each file only one time:

awk '
    # read the list of numbers in truncations_list
    FNR == NR {
        num[$1]
        next
    }

    # process each line of the output file
    # any lines with an "unknown" $12 will be ignored
    $12 in num {
        f = "reads_" $12 ".txt"
        print >> f
    }
' truncations_list.txt R2_Output.txt

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