how to direct a sh script to run a python script?

Question

I wrote a python script that calls two files to perform some calculations and asks for a name for the new file to place the calculation in so my code runs like this:

python code.py in_file1 in_file2 outfile

Now, I have several files that need the same calculation and their names only change by the last numbers, so I wanted to do a script that takes the different needed files in a folder performs the python script and name the outputs changing only the las number according to the given in_file1 (infield_2 actually does not change).

I tried something simple but is not working

#!/bin/bash
python code.py in_file[19]* infile_2 outfile[19]*

I get an error from the usage of python saying that usage: python code.py [-h] in in2 out unrecognized arguments

I know for sure that code.py works, I just wanted to spare to do it one file at a time. Thank you. I am really new in python and linux, appreciate any help you can give.

Does code.py output something? Is it absolutely necessary to write the script in BASH? It can be written in Python too — ForceBru
– ForceBru, Commented Apr 14, 2015 at 15:55
Yes, it performs the calculations and outputs it in a file which name I choose as outfile, Is not necessary to do it in BASH, I just want to spare to do it one by one — pepa
– pepa, Commented Apr 14, 2015 at 15:58

ForceBru · Accepted Answer · 2015-04-14 16:08:22Z

1

You can do the same in Python

from subprocess import call

fname="in_file{} infile2 outfile{}"
for x in xrange(1,11):
    d=call(["python","code.py",fname.format(x,x)])
    if d:
        print "Error executing: {}".format(d)

If you execute the following

fname="in_file{}"
for x in xrange(1,11):
    print ["python","code.py",fname.format(x)]

It will print the following

['python', 'code.py', 'in_file1']
['python', 'code.py', 'in_file2']
['python', 'code.py', 'in_file3']
['python', 'code.py', 'in_file4']
['python', 'code.py', 'in_file5']
['python', 'code.py', 'in_file6']
['python', 'code.py', 'in_file7']
['python', 'code.py', 'in_file8']
['python', 'code.py', 'in_file9']
['python', 'code.py', 'in_file10']

edited Apr 14, 2015 at 16:08

answered Apr 14, 2015 at 15:59

ForceBru

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Comments

tripleee · Accepted Answer · 2015-04-14 16:26:11Z

The shell simply expands the wildcard in_file[19]* there and then into list of all matching files. There is no loop here. If you want a loop, you will need an explicit loop, something like

#!/bin/bash
for file in in_file[19]*; do
    python code.py "$file" infile_2 "out${file#in}"
done

where the variable file gets assigned to each matching file in turn, and the variable substitution ${var#prefix} expands to the value of var with any string prefix removed from the beginning.

Incidentally, the python is redundant if you make code.py executable, and ensure it has a correct shebang line.

Note also that [19] matches a single character, so your wildcard matches any files whose name starts with in_file1 or in_file9 but no others. I'm speculating maybe that's not what you mean.

A.J. Uppal · Accepted Answer · 2015-04-14 16:00:48Z

0

You can do this in python:

import os

name = "in_file%d"
for i in range(1, 21):
    os.system("python code.py in_file{} in_file2 outfile{}".format(i, i))

This works as the following, with the os library calling the outputted strings:

>>> for i in range(1, 21):
...     "python code.py in_file{} in_file2 outfile{}".format(i, i)
... 
'python code.py in_file1 in_file2 outfile1'
'python code.py in_file2 in_file2 outfile2'
'python code.py in_file3 in_file2 outfile3'
'python code.py in_file4 in_file2 outfile4'
'python code.py in_file5 in_file2 outfile5'
'python code.py in_file6 in_file2 outfile6'
'python code.py in_file7 in_file2 outfile7'
'python code.py in_file8 in_file2 outfile8'
'python code.py in_file9 in_file2 outfile9'
'python code.py in_file10 in_file2 outfile10'
'python code.py in_file11 in_file2 outfile11'
'python code.py in_file12 in_file2 outfile12'
'python code.py in_file13 in_file2 outfile13'
'python code.py in_file14 in_file2 outfile14'
'python code.py in_file15 in_file2 outfile15'
'python code.py in_file16 in_file2 outfile16'
'python code.py in_file17 in_file2 outfile17'
'python code.py in_file18 in_file2 outfile18'
'python code.py in_file19 in_file2 outfile19'
'python code.py in_file20 in_file2 outfile20'
>>>

answered Apr 14, 2015 at 16:00

A.J. Uppal

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4 Comments

ForceBru Over a year ago

Exact copy of my answer, isn't it? :)

A.J. Uppal Over a year ago

@ForceBru, nope. Open your eyes.

pepa Over a year ago

Thank you everybody :D it worked :D Your answers helped me a lot :)

A.J. Uppal Over a year ago

@pepa if this answer helped you, would you mind accepting it? Click on the green check next to my answer (it gives you reputation too) :)

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