your_script.bat:

set VAR_1=this
set VAR_2=that

python your_script.py %1 %VAR_1% %VAR_2%

c:\python27\python.exe c:\somescript.py %*

Python is similar.

import os
os.system("run-client.bat param1 param2")

If you need asynchronous behavior or redirected standard streams.

from subprocess import *
p = Popen(['run-client.bat', param1, param2], stdout=PIPE, stderr=PIPE)
output, errors = p.communicate()
p.wait() # wait for process to terminate

Replace test with "${filename%.faa}" to get the name of the file with .faa removed. You should also quote "${filename}" to avoid problems in case of filenames with spaces.

#!/bin/sh
for filename in *.faa ; do
    python predict_genome.py \
        --fasta_path /Users/mvalvano/DeepSecE/myruns/"${filename}" \
        --model_location /Users/mvalvano/DeepSecE/model/checkpoint.pt \
        --data_dir data \
        --out_dir myruns/"${filename%.faa}" \
        --save_attn --no_cuda
    done
exit 0

With input files

bar.faa
foo.faa

the script will run

python predict_genome.py --fasta_path /Users/mvalvano/DeepSecE/myruns/bar.faa --model_location /Users/mvalvano/DeepSecE/model/checkpoint.pt --data_dir data --out_dir myruns/bar --save_attn --no_cuda
python predict_genome.py --fasta_path /Users/mvalvano/DeepSecE/myruns/foo.faa --model_location /Users/mvalvano/DeepSecE/model/checkpoint.pt --data_dir data --out_dir myruns/foo --save_attn --no_cuda

Possible problems with this script:

Since you specify --fasta_path /Users/mvalvano/DeepSecE/myruns/"${filename}", your script will only work without error if the current directory is /Users/mvalvano/DeepSecE/myruns/ or if this directory contains at least the same set of *.faa files as the current directory. (*.faa will expand to the file names in the current directory.)

When /Users/mvalvano/DeepSecE/myruns/ is the current directory, the argument --out_dir myruns/foo might expect or create a directory /Users/mvalvano/DeepSecE/myruns/myruns/foo with double myruns.