Pass arguments as a list, see the very first code example in the docs:

import subprocess

subprocess.check_call(['/my/file/path/programname.sh', 'arg1', 'arg2', arg3])

If arg3 is not a string; convert it to string before passing to check_call(): arg3 = str(arg3).

To execute a python script in a bash script you need to call the same command that you would within a terminal. For instance

> python python_script.py var1 var2

To access these variables within python you will need

import sys
print(sys.argv[0]) # prints python_script.py
print(sys.argv[1]) # prints var1
print(sys.argv[2]) # prints var2

The python equivalent of the shell's positional parameter array $1, $2 etc. is sys.argv

So:

#!/usr/bin/env python

import sys

def getPermutation(s, prefix=''):
        if len(s) == 0:
                print prefix
        for i in range(len(s)):
                getPermutation(s[0:i]+s[i+1:len(s)],prefix+s[i] )



getPermutation(sys.argv[1],'')

then

$ ./foo.py abcd
abcd
abdc
acbd
acdb
adbc
adcb
bacd
badc
bcad
bcda
bdac
bdca
cabd
cadb
cbad
cbda
cdab
cdba
dabc
dacb
dbac
dbca
dcab
dcba

Because shell script has no way of knowing that you want to pass arguments to your Python script. Use

./Main.py "$@"

Also don't use cd. It's redundant. Just use full path to ./Main.py , or even better avoid having a wrapper script altogether, unless necessary. Just put ./Main.py into one of the directories that are part of your $PATH variable and call your Python script directly.

The main point is that what you're trying to do is probably wrong and unnecessary, and there are better ways to do it

You can also use the sys module. Here is an example :

import sys

first_arg = sys.argv[1]
second_arg = sys.argv[2]

def greetings(word1=first_arg, word2=second_arg):
    print("{} {}".format(word1, word2))

if __name__ == "__main__":
    greetings()
    greetings("Bonjour", "monde")

It has the behavior your are looking for :

$ python parse_args.py Hello world
Hello world
Bonjour monde

Fixed here: #2689

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.

Perhaps the aws bash command is returning non-printable characters that you don't see with print(). Try removing them with tr:

FOLDER=$(./aws get $BUCKET"/location.txt" | tr -cd "[:print:]")