嵌套的awk命令? [英] nested awk commands?

问题描述

我有以下两个代码:

nut=`awk "/$1/{getline; print}" ids_lengths.txt`

和

grep -v '#' neco.txt |
grep -v 'seq-name' |
grep -E '(\S+\s+){13}\bAC(.)+CA\b' |
awk '$6 >= 49 { print }' |
awk '$6 <= 180 { print }' |
awk '$4 > 1 { print }' |
awk '$5 < $nut { print }' |
wc -l

我希望我的脚本在此处替换"nut":

I would like my script to replace "nut" at this place:

awk '$4 < $nut { print }'

，其中包含从此返回的数字:

with the number returned from this:

nut=`awk "/$1/{getline; print}" ids_lengths.txt`

但是，上面代码中的$ 1应该不是ids_lengths.txt中的列，而是neco.txt中的第一列！ (就像我在主代码中使用$ 6和$ 4一样.)

However, $1 in code just above should represent not column from ids_lengths.txt, but first column from neco.txt! (similiarly as I use $6 and $4 in main code).

将非常感谢您提供帮助来解决这些嵌套的awks:-)

A help how to solve these nested awks will definitely be appreciated:-)

我的输入文件(neco.txt)的行如下所示:

edit: Line of my input file (neco.txt) looks like this:

FZWTUY402JKYFZ  2   100.000 3   11  9     4.500 7   0   0   0   .   TG  TGTGTGTGT

最大的问题是，在第一列(例如FZWTUY402JKYFZ)中进行搜索时，我想过滤那些第五列中的行号小于number的行，这些行是从另一个文件(ids_lengths.txt)获得的.这就是为什么我在草稿脚本中放入"nut"变量的原因:-)

The biggest problem is that I want to filter those lines that have in the fifth column number less than number, which I get from another file (ids_lengths.txt), when searching with first column (e.g. FZWTUY402JKYFZ). That's why I put "nut" variable in my draft script :-)

ids_lengths.txt看起来像这样:

ids_lengths.txt looks like this:

>FZWTUY402JKYFZ 
153
>FZWTUY402JXI9S 
42
>FZWTUY402JMZO4 
158

推荐答案

您可以将两个grep -v操作和四个连续的awk操作组合在一起.这可为您带来有用的经济效益，而无需完全重写所有内容:

You can combine the two grep -v operations and the four consecutive awk operations into one of each. This gives you useful economy without completely rewriting everything:

nut=`awk "/$1/{getline; print}" ids_lengths.txt`
grep -E -v '#|seq-name' neco.txt |
grep -E '(\S+\s+){13}\bAC(.)+CA\b' |
awk -vnut="$nut" '$6 >= 49 && $6 <= 180 && $4 > 1 && $5 < nut { print }' |
wc -l

我不会费心让单个awk脚本确定nut的值并进行基于值的过滤.可以做到，但是却不必要地使事情复杂化-除非您可以证明整个事情是生产系统性能的瓶颈，否则这种情况下您会更加努力地工作(尽管在这种情况下我可能会使用Perl；它会只需一个命令就可以完成全部任务.)

I would not bother to make a single awk script determine the value of nut and do the value-based filtering. It can be done, but it complicates things unnecessarily — unless you can demonstrate that the whole thing is a bottleneck for the performance of the production system, in which case you do work harder (though I'd probably use Perl in that case; it can do the whole lot in one command).

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