For loop with two input files

Question

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

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

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

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

codeforester · Accepted Answer · 2017-03-29 18:29:13Z

1

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

answered Mar 29, 2017 at 18:29

codeforester

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2 Comments

Ryan Zapotocny Over a year ago

Thanks this works great. I am having issues with the naming of these files now. I will edit my post to address this

Ryan Zapotocny Over a year ago

Solved: Just change $f in the pref line to $f1. Thank you for your help

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