Expanding an array within a for loop (file list) - arrays

Question

I am running into problems when interating over files using a for-loop. For simplicity, I created a small loop which should explain which problem I have at the moment.
Starting point: files in a folder which have a file-specific one to three digit number at a defined position in their filename.
Goal: Iterate over some of these files (not all) using a for-loop.
Problem: I created an array containing these one to three digit numbers specific for each file. The files are called at the beginning of the for-loop and I would like to use the array to reference to the specific files. But: The array is not expanding correctly.
Hope someone can help!
(There might be several good alternative ways to do this. Maybe some of them do not need an array, but I would be interested in knowing the solution to my specific problem since I think this might be a fundamental missunderstanding in how to expand a variable as part of filenames at the beginning of a for-loop.)
This is the code:
declare -a SOME_SAMPLES=(37 132 253 642 242 42)
for d in prmrp_*_${SOME_SAMPLES[#]}_S*_L00?_R1_001.fastq.gz; do
INPUT_FILE1=$(echo $d | sed 's/_L00._R1_001.fastq.gz//')
echo ${INPUT_FILE1}
done
Again, this is just an example code. The problem is the ${SOME_SAMPLES[#]} part which is not expanding correctly so the loop fails.
Thanks!

Answer 1

I think the problem is that in
prmrp_*_${SOME_SAMPLES[#]}_S*_L00?_R1_001.fastq.gz
it doesn't duplicate the entire expression for each element of the array, it just blindly inserts the array's elements in the middle, giving the equivalent of this:
prmrp_*_37 132 253 642 242 42_S*_L00?_R1_001.fastq.gz
... which is a bunch of separate items (prmrp_*_37 as a wildcard expression, followed by 132 as a simple string, followed by 253 etc). AIUI you want to expand the array's contents, and then for each element use a wildcard expression to get all matching files. The best way to do this is to use two loops, one to expand the array, and another to find matching files:
for sample in "${SOME_SAMPLES[#]}"; do
for d in prmrp_*_"${sample}"_S*_L00?_R1_001.fastq.gz; do
...
BTW, I'd also recommend using lowercase or mixed-case variable names (e.g. sample above) to avoid possible conflicts with the many all-caps variables with special meanings/functions. Also, I'd use a parameter expansion to remove the filename's suffix (instead of sed):
input_file1=${d%_L00?_R1_001.fastq.gz}
Also, you should generally put double-quotes around variable references (e.g. echo "${input_file1}" instead of echo ${input_file1}). (Assignments like input_file1=${d... are an exception, although double-quotes don't hurt there; they just aren't needed.) Note that in the for loop above, I put double-quotes around the array and variable references, but not around the wildcards; this means the shell will expand the wildcards (as you want) but not mess with the variable's contents.

Answer 2

Try:
array=( 37 132 253 642 242 42 );
for d in ${array[#]}; do
INPUT_FILE1="prmrp_*_"$d"_S*_L00?_R1_001.fastq.gz";
echo ${INPUT_FILE1}
done