loop through list element one at the time

Question

Hi there I've been experimenting with a job array using Singularity, the problem is that singularity takes in input only global/environment variables within the container — to the best of my knowledge at least.

So, my problem is that I have to generate a string, assign it to a variable, which contains the paths where my files live and I have to do this for 279 time. My first naïve attempt was the following:

for i in {1..279};
do
        SAMPLE="ls /path/to/sgdp_$i/input/*_chr.bam"
done

Of course, what I get out of this is that the for runs through the the entire loop up until the 279th iteration and the folder sgdp_279 doesn't contain the actual BAM file I'm looking for in the first folder, named sgdp_001, and which is the first one visited by the job array.

Essentially, what I would need is an iterator which generates the former path along with the array, or that iterates only once at the time without running through the entire loop in one go. I hope I explained the issue clearly, please if you need further details I can share the entire code. I've attempted several other options, unsuccessfully... thanks in advace for your help!

EDIT - answer to @jhnc

Good point this is the tree -h of my sgdp directories

sgdp_001
├── [ 4.0K]  input
│   ├── [  83G]  abh100_chr.bam
│   └── [ 8.5M]  abh100_chr.bam.bai
├── [ 4.0K]  output
├── [  83G]  sample_chr.bam
└── [ 8.5M]  sample_chr.bam.bai
sgdp_002
├── [ 4.0K]  input
│   ├── [  79G]  abh107_chr.bam
│   └── [ 8.5M]  abh107_chr.bam.bai
├── [ 4.0K]  output
├── [  79G]  sample_chr.bam
└── [ 8.5M]  sample_chr.bam.bai
.
.
.

The desired output for the former two cases should be

/path/to/sgdp_001/input/abh100_chr.bam
/path/to/sgdp_002/input/abh107_chr.bam

caveat is the BAM files all have different prefix before the _chr.bam sequence.

Answer 1

Try either of these:

for SAMPLE in /path/to/sgdp_*/input/*_chr.bam
    stuff with "$SAMPLE"
done

or:

while IFS= read -d '' -r SAMPLE; do
    stuff with "$SAMPLE"
done < <(printf '%s\0' /path/to/sgdp_*/input/*_chr.bam)

or:

while IFS= read -d '' -r SAMPLE; do
    stuff with "$SAMPLE"
done < <(find /path/to/sgdp_*  -type f -name '*_chr.bam' -print0)

or:

for dir in /path/to/sgdp_*; do
    while IFS= read -d '' -r SAMPLE; do
        stuff with "$SAMPLE"
    done < <(find "$dir" -type f -name '*_chr.bam' -print0)
done