Bash script: how to stop looping after a match was found? - regex

Question

This must be very basic but I can't not find a way to solve it.
I have a script like this:
#!/bin/bash
seqFolder="/raw_data/data"
seqmode="paired"
Input=$(basename ${seqFolder});
if [ $seqmode = paired ]; then
for x in $seqFolder/*; do
if [[ "$x" =~ .*\.fastq.gz$ ]]; then
z=$(basename $x 1_001.fastq.gz)
echo $z
echo "file of this iteration $z"1_001.fastq.gz" $z"2_001.fastq.gz""
fi
done
fi
When I run this script I get this:
MG-AB-17_S17_R
file of this iteration MG-AB-17_S17_R1_001.fastq.gz MG-AB-17_S17_R2_001.fastq.gz
MG-AB-17_S17_R2_001.fastq.gz
file of this iteration MG-AB-17_S17_R2_001.fastq.gz1_001.fastq.gz MG- AB-17_S17_R2_001.fastq.gz2_001.fastq.gz
MG-AB-81_S74_R
file of this iteration MG-AB-81_S74_R1_001.fastq.gz MG-AB-81_S74_R2_001.fastq.gz
MG-AB-81_S74_R2_001.fastq.gz
file of this iteration MG-AB-81_S74_R2_001.fastq.gz1_001.fastq.gz MG- AB-81_S74_R2_001.fastq.gz2_001.fastq.gz
Files in: /raw_data/data are these 4 (this is just example):
MG-AB-17_S17_R1_001.fastq.gz
MG-AB-17_S17_R2_001.fastq.gz
MG-AB-81_S74_R1_001.fastq.gz
MG-AB-81_S74_R2_001.fastq.gz
The issue is that I don't want my variable $z to be MG-AB-17_S17_R2_001.fastq.gz or MG-AB-81_S74_R2_001.fastq.gz because files like these:
MG-AB-17_S17_R2_001.fastq.gz1_001.fastq.gz
MG-AB-17_S17_R2_001.fastq.gz2_001.fastq.gz
...
don't exist in directory /raw_data/data
I was thinking that .fastq.gz$ in "$x" =~ .*\.fastq.gz$ would ensure that, but it seems that's not the case. Can you please advise.

Answer 1

You're looking for the break statement.
$ cat /tmp/so3651.sh
#!/usr/bin/env bash
for i in 1 2 3 4 5; do
echo "i: $i"
if [[ -f /tmp/foo$i ]]; then
echo "found it!"
break
fi
done
If the file doesn't exist, it produces:
$ /tmp/so3651.sh
i: 1
i: 2
i: 3
i: 4
i: 5
But when a file does exist, it stops early:
$ touch /tmp/foo4
$ /tmp/so3651.sh
i: 1
i: 2
i: 3
i: 4
found it!