Question

我有一个小的示例数据集test1.faa

>PROKKA_00001_A1@hypothetical@protein
MTIALHLTAVLAFAALAGCGANDSDPGPGGVTVSEARALDQAAEMLEKRGRSPADENAEQAERLRREQAQARTPGQPPEQALQQDGASAPE
>PROKKA_00002_A1@Cystathionine@beta-lyase
MHRFGGMVTAILKGGLDDARRFLERCELFALAESLGGVESLIEHPAIMTHASVPREIREALGISDGLVRLSVGIEDADDLLAELETALA
>PROKKA_00003_A1@hypothetical@protein
MVPIVSAAPVFTLLLTVAVFRRERLTAGRIAAVAVVVPSVILIALGH

，我想将以下行的长度添加到标题行，然后添加下一行，例如

>PROKKA_00001_A1@hypothetical@protein_92
MTIALHLTAVLAFAALAGCGANDSDPGPGGVTVSEARALDQAAEMLEKRGRSPADENAEQAERLRREQAQARTPGQPPEQALQQDGASAPE

我尝试使用awk进行此操作，但它返回以下错误：

awk: >PROKKA_00001_A1@hypothetical@protein: No such file or directory

我假设它在一开始就与>有关？但是我需要在输出文件中。

这是我尝试的代码：

#!/bin/bash

cat test1.faa | while read line
do
  headerline=$(awk '/>/{print $0}' $line)
  echo -e "this is the headerline \n ${headerline}"
  fastaline=$(awk '!/>/{print $0}' $line)
  echo -e "this is the fastaline \n ${fastaline}"
  fastaline_length=$(awk -v linelength=$fastaline '{print length(linelength)}')
  echo -e "this is length of fastaline \n ${fastaline_length}"
  echo "${headerline}_${fastaline_length}"
  echo $fastaline
done

有关如何执行此操作的任何建议？

Answer 1

请尝试以下操作（考虑到您的实际Input_file与所示示例相同）。

awk '/^>/{value=$0;next} {print value"_"length($0) ORS $0;value=""}' Input_file

Answer 2

此awk命令将完成您想要的

Col1   |  Col2   |  Col3   |  Col4   
------------------------------------
Row1C1 | Row1C2  | Row1C3  | Row1C4
Row2C1 | Row2C2  | Row2C3  | Row2C4
Added static row here with colspan
Row3C1 | Row3C2  | Row3C3  | Row3C4
Row4C1 | Row4C2  | Row4C3  | Row4C4

在bash中将以下行的长度添加到当前行

2 个答案: