带两个输入文件的For循环 [英] For loop with two input files

问题描述

我希望对需要两个输入文件的命令使用for循环.两个文件之间只有一个字符更改.这是两个示例文件:

I wish to use a for loop for a command that requires two input files. There is a single character change between the two files. Here are two example files:

Fay2_TCCGGAGA-CCTATCCT_L001_R1_001.fastq
Fay2_TCCGGAGA-CCTATCCT_L001_R2_001.fastq

这是我尝试执行的命令:

Here is my attempt of the command:

for f in /directory/*R1*.fastq
 pref=${basename "$f" _*R1*.fastq}
command input1 $f input2 ${pref}_*R2*.fastq

问题很可能在于操纵基名称，因此循环使用file1的排列来查找file2.如何使基本名称比整个文件名短.我收到错误

The issue most likely lies in manipulating the basename so the loop uses the permutation of file1 to find file2. How do I make the basename shorter than the entire file name. I am getting the error

Fay2_TCCGGAGA-CCTATCCT_L001_R2_001.fastq_*R2.fastq does not exist

由于下面的注释，循环正常工作，但是每当命令循环一个新文件时，我的文件就会被覆盖.以下是我的整个命令，需要命名两个输出文件.

Thanks to comments below the looping is working properly but my files are being overwritten whenever a the command loops over a new file. The following is my entire command which requires naming both output files.

for f1 in /directory/*R1*.fastq
f2="${f1/_R1_/_R2_}"
 pref=${basename "$f" _*R1*.fastq}
command output1 ${pref}_trim_R1.fastq output2 ${pref}_trim_R2.fastq input1 $f input2 $f2

推荐答案

您可以循环浏览R1文件并使用大括号扩展来得出R2文件名:

You can loop through the R1 files and use brace expansion to derive R2 file names:

for r1_file in /directory/*_R1_*.fastq; do
  r2_file="${r1_file/_R1_/_R2_}"
  command input1 "$r1_file" input2 "$r2_file"
done

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