grouping input files with incremental names to divide a computation into smaller ones - linux

Question

I created a script to run a function that takes a specific file and compares it to several others. The files that I have to scan for the matches are more than 900 and incrementally named like this:
A001-abc.txt A001-efg.txt [..] A002-efg.txt A002-hjk.txt [..] A120-xwz.txt (no whitespaces)
The script looks like this:
#!/bin/bash
for f in *.txt; do
bedtools function /mydir/myfile.txt *.txt> output.txt
done
Now, the computation is extremely intensive and can't be completed. How can I group the files according to their incremental name and perform the computation on files A001-abc A001-def then go to A002-abc, A002-def.., to A123-xyz and so on?
I was thinking that by finding a way to specify the name with an incremental variable and then grouping them, I could divide the computation in many smaller ones. Is it reasonable and doable?
Many thanks!

Answer 1

The problem might be that you're not using $f. Try using this line in the for-loop instead. Also, use >> so the output appends instead of overwriting the output file.
bedtools function /mydir/myfile.txt "$f" >> output.txt
But if you still want to break it up, you might try a double loop like this:
for n in $(seq --format="%03.f" 1 120); do
for f in "A$n"*; do
bedtools function /mydir/myfile.txt "$f" >> "${n}output.txt"
done
done
The values of $n from the output of the seq command is 001 002 .. 120.
So the inner loop loops through A001* A002* .. A120*.