How to take substring from input file as an argument to a program to be executed in GNU-parallel? - gnu-parallel

Question

I am trying to execute a program (say, biotool) using GNU-parallel which takes 3 arguments, i, o and a :
the input files (i)
output file name to be written in (o)
an argument which takes a sub string from the input file name (a)
for example, say i have 10 text files like this
1_a_test.txt
2_b_test.txt
3_c_test.txt
...
10_j_test.txt
I want to run my tool (say biotool) on all the 10 text files. I tried this
parallel biotool -i {} -o {.}.out -a {} ::: *.txt
I want to pass the charachter/letter/whatever before the first underscore from the input text file name as an argument to -a option like this (dry run):
parallel biotool -i 1_a_test.txt -o 1_a_test.out -a 1 ::: *.txt`
parallel biotool -i 2_b_test.txt -o 2_b_test.out -a 2 ::: *.txt`
parallel biotool -i 3_c_test.txt -o 3_c_test.out -a 3 ::: *.txt`
...
{} supplies the complete file name to -a but I only want the sub string before the first underscore to be supplied to -a

Answer 1

The easiest, but harder to read is this:
parallel --dry-run biotool -i {} -o {.}.out -a '{= s/_.*// =}' ::: *test.txt
Alternatively, you can make a bash function that uses bash Parameter Substitution to extract the part before the underscore. Then export that to make it known to GNU Parallel
#!/bin/bash
doit(){
i=$1
o=$2
# Use internal bash parameter substitution to extract whatever precedes "_"
# See https://www.tldp.org/LDP/abs/html/parameter-substitution.html
a=${i/_*/}
echo biotool -i "$i" -o "$o" -a "$a"
}
export -f doit
parallel doit {} {.}.out ::: *test.txt
Sample Output
biotool -i 10_j_test.txt -o 10_j_test.out -a 10
biotool -i 1_a_test.txt -o 1_a_test.out -a 1
biotool -i 2_b_test.txt -o 2_b_test.out -a 2