How do I make wildcards work in a bash script - bash

Question

I am trying to run a bash script:
#~/bin/sh
mkdir metaphlan2
echo "Profiling from reads"
echo
samples="CFC280618 MFC280618 SBW280618"
for x in ${samples}
do metaphlan2.py ${x}_S*_R1_001.fastq.gz,${x}_S*_R2_001.fastq.gz --bowtie2out metaphlan2/\${x}.bowtie2.bz2 -o metaphlan2/\${x}.metaphlan2.txt --input_type multifastq --nproc 10
done
Where the * is supposed to represent any character.
However when I ran my script in terminal, I got the following error:
IOError: [Errno 2] No such file or directory: 'SBW280618_S*_R1_001.fastq.gz'
Will anyone be kind enough to help please?
Thank you.

Answer 1

The * is not supposed to represent any character, but to expand the string to match something that exists by substituting the * for whatever is needed.
Unfortunately, you are trying to expand
${x}_S*_R1_001.fastq.gz,${x}_S*_R2_001.fastq.gz
and probably you don't have any file called that way. I'm pretty sure you have two files, one called ${x}_S*_R1_001.fastq.gz and another called ${x}_S*_R2_001.fastq.gz. The comma in the middle make that string to be considered a single string/file.
You need to separate the files between them with spaces. If that's not possible, you will have to expand both files independently and finally generate the string your binary needs.
Try with this second option:
#/bin/sh
mkdir metaphlan2
echo "Profiling from reads"
echo
samples="CFC280618 MFC280618 SBW280618"
for x in ${samples}
do
fq1="${x}"_S*_R1_001.fastq.gz
fq2="${x}"_S*_R2_001.fastq.gz
metaphlan2.py "$fq1,$fq2" --bowtie2out metaphlan2/\${x}.bowtie2.bz2 -o metaphlan2/\${x}.metaphlan2.txt --input_type multifastq --nproc 10
done