Question

I have never programed in bash before.
I am reading all the files that are in a directory, then I need to look into their names and check if the have R1 or R2, depending on that I need concatenate all files that have R1 in the same and all files that have R2 in the name.
So as a final output I would like to have something like:

String 1 = file1_R1.gz file2_R1.gz file3_R1.gz…

String 2 = file1_R2.gz file2_R2.gz file3_R2.gz…

how can I do that? the only code that I have so far is:

#!/bin/bash

list=$(echo *.gz)

strR1="R1"
strR2="R2"

if [ "$list" = "*.gz" ] ; then list=""; fi

for str in $list
do
    if echo "$strR1"  | grep -q "$str"; then
         echo "str";
else 
echo "no file";
fi

done

I can read all the files in the directory but when I do the if I cannot find any file with R1, and I know that there are at least 4 files with R1 in the name.

Thank you!

Answer 1

Why write a loop to do the filtering wildcards will already do for you? (You’re using the same thing to filter *.gz already.)

files1=`echo *R1*.gz`
files2=`echo *R2*.gz`

Since you said you want to concatenate all those files, that would then be

zcat *R1.gz > result_R1
zcat *R2.gz > result_R2

or something like that.