linux for loop two variables each time - bash

Question

I have several files in a directory and I want to run some linux packages on these files by every two of them, like ERR1045141_1 with ERR1045141_2 and ERR1045144_1 with ERR1045144_2 and so on. So I write a for loop for this but it is not working.
files:
ERR1045141_1.fastq.gz
ERR1045141_2.fastq.gz
ERR1045144_1.fastq.gz
ERR1045144_2.fastq.gz
ERR1045145_1.fastq.gz
ERR1045145_2.fastq.gz
ERR1045146_1.fastq.gz
ERR1045146_2.fastq.gz
ERR1045148_1.fastq.gz
ERR1045148_2.fastq.gz
ERR1045149_1.fastq.gz
ERR1045149_2.fastq.gz
ERR1045151_1.fastq.gz
ERR1045151_2.fastq.gz
ERR1045152_1.fastq.gz
ERR1045152_2.fastq.gz
ERR1045154_1.fastq.gz
ERR1045154_2.fastq.gz
codes:
files=ls
for (( i=0; i<${#files[#]} ; i+=2 )) ; do
echo "${files[i]}" "${files[i+1]}"
done
It did not work and I am not sure is the files=ls has something wrong.Or any better way to do it.please advise.

Answer 1

Try the following if you are sure about the existence of the second file:
for file1 in ERR*_1*
do
file2=`echo $file1 | sed 's/_1/_2/g'`
echo $file1 $file2
done

Answer 2

No, what you really want to do is to process all the 1 files, performing some action on it and its associated 2 file.
You can do that with something as simple as the for loop in this complete test program:
#!/usr/bin/env bash
doSomethingWith() {
echo "[$1] [$2]"
}
touch 'xERR1045141_1.fastq.gz' 'xERR1045141_2.fastq.gz'
touch 'xERR1045144_1.fastq.gz' 'xERR1045144_2.fastq.gz'
touch 'xERR1045145_1.fastq.gz' 'xERR1045145_2.fastq.gz'
touch 'xERR1045146_1.fastq.gz' 'xERR1045146_2.fastq.gz'
touch 'xERR1045148_1.fastq.gz' 'xERR1045148_2.fastq.gz'
touch 'xERR1045149_1.fastq.gz' 'xERR1045149_2.fastq.gz'
touch 'xERR1045151_1.fastq.gz' 'xERR1045151_2.fastq.gz'
touch 'xERR1045152_1.fastq.gz' 'xERR1045152_2.fastq.gz'
touch 'xERR1045154_1.fastq.gz' 'xERR1045154_2.fastq.gz'
touch 'xERR 45154_1.fastq.gz' 'xERR 45154_2.fastq.gz'
for file1 in xERR*_1.fastq.gz ; do
file2="${file1/_1/_2}"
doSomethingWith "${file1}" "${file2}"
done
rm -rf xERR*.fastq.gz
This program outputs:
[xERR1045141_1.fastq.gz] [xERR1045141_2.fastq.gz]
[xERR1045144_1.fastq.gz] [xERR1045144_2.fastq.gz]
[xERR1045145_1.fastq.gz] [xERR1045145_2.fastq.gz]
[xERR1045146_1.fastq.gz] [xERR1045146_2.fastq.gz]
[xERR1045148_1.fastq.gz] [xERR1045148_2.fastq.gz]
[xERR1045149_1.fastq.gz] [xERR1045149_2.fastq.gz]
[xERR1045151_1.fastq.gz] [xERR1045151_2.fastq.gz]
[xERR1045152_1.fastq.gz] [xERR1045152_2.fastq.gz]
[xERR1045154_1.fastq.gz] [xERR1045154_2.fastq.gz]
[xERR 45154_1.fastq.gz] [xERR 45154_2.fastq.gz]
to show that the names are being handled correctly.
Note that I've named the files xERR* so as not to clash with your own files. You should adjust the loop to handle your own files once you're satisfied it will work okay.
And, just as an aside, if you don't want to do anything except for those cases where both files exist, you can simply replace the "action" line with something like:
[[ -f "${file2}" ]] && doSomethingWith "${file1}" "${file2}"
This will bypass those where the 2 file is not a regular file.