Read several files from command line

Question

My code name is Test.py and it contains:

#! /usr/bin/python3.8
import sys                          
import numpy as np                  
from numpy import loadtxt           
from numpy import savetxt
import math                         
import pandas as pd                 

filename = open(sys.argv[1], "r")
Matriz = loadtxt(sys.argv[1], comments="#", delimiter=",", unpack=False)
filename.close()

filename = open(sys.argv[1], "r")
Atomos = loadtxt(sys.argv[1], comments="#", delimiter=",", unpack=False)
filename.close()

print(np.array(Matriz))
print(np.array(Atomos))

The content of both files is:

Matriz

-0.0348687198,0.1076326826,0.0000843068
0.0573782020,1.3095730862,0.0000068272
1.0254494561,-0.7164980418,0.0000085392
2.2996131174,-0.0921357246,-0.0000447488
3.0330746822,-0.8942281572,-0.0001369182
2.4148217507,0.5343388106,-0.8871728184
2.4149308325,0.5342246938,0.8871497899
-1.2975203980,-0.6615612550,0.0000051853
-2.4725470102,-0.0497367819,-0.0000446353
-3.4040644912,-0.5890411227,0.0000073839
-2.5208587260,1.0272815633,-0.0001277685
-1.1879865504,-1.7352844954,0.0000351158

Atomo

C
O
O
C
H
H
H
C
C
H
H
H

and I ran my code like: ./Test.py Matriz Atomo' and it only print the content of Matriz.

How can I make my code to read two or more files in command line?

I tried it:

filename = open(sys.argv[1], "r")
Matriz = loadtxt(sys.argv[1], comments="#", delimiter=",", unpack=False)
filename.close()

filename = open(sys.argv[2], "r")
Atomos = loadtxt(sys.argv[2], comments="#", delimiter=",", unpack=False)
filename.close()

and I get:

Traceback (most recent call last):
  File "./E_State.py", line 15, in <module>
    Atomos = loadtxt(sys.argv[2], comments="#", delimiter=",", unpack=False)
  File "/usr/lib/python3/dist-packages/numpy/lib/npyio.py", line 1146, in loadtxt
    for x in read_data(_loadtxt_chunksize):
  File "/usr/lib/python3/dist-packages/numpy/lib/npyio.py", line 1074, in read_data
    items = [conv(val) for (conv, val) in zip(converters, vals)]
  File "/usr/lib/python3/dist-packages/numpy/lib/npyio.py", line 1074, in <listcomp>
    items = [conv(val) for (conv, val) in zip(converters, vals)]
  File "/usr/lib/python3/dist-packages/numpy/lib/npyio.py", line 781, in floatconv
    return float(x)
ValueError: could not convert string to float: 'C'

Does this answer your question? [sys.argv\[1\] meaning in script](https://stackoverflow.com/questions/4117530/sys-argv1-meaning-in-script) — May.D, Jul 02 '21 at 20:28
Good explanation, but I cannot translate it to my needs, would you help me? please (I am a beginner, self-taught) — Another.Chemist, Jul 02 '21 at 20:34
I'm curious why you didn't try changing [1] to [2] for the second file!? — mkrieger1, Jul 02 '21 at 20:34
What do you mean by "it did not work"? Was there an error message? — mkrieger1, Jul 02 '21 at 20:35
Just a suggestion, It could be better if you use Argparse module instead of Sys module to read arguments entered on command line. It's neater and have more funcions (It reads every word separate by spaces for example) — Diroallu, Jul 02 '21 at 20:35
Another suggestion is to use context managers (with the keyword `with`) so you dont have to manually close the files. — May.D, Jul 02 '21 at 20:38
Well now it becomes apparent that the actual problem is not how to pass two different filenames to the program, but that you tried to use `numpy.loadtxt` to load a file that doesn't contain numbers. — mkrieger1, Jul 02 '21 at 20:41
Does this answer your question? [How to read a file line-by-line into a list?](https://stackoverflow.com/questions/3277503/how-to-read-a-file-line-by-line-into-a-list) — mkrieger1, Jul 02 '21 at 20:44
Why not? What is missing? Did you even read all 28 answers before dismissing them all? — mkrieger1, Jul 02 '21 at 20:46
@mkrieger1 that link show how to operate on one open file and I want to open several files from command line — Another.Chemist, Jul 02 '21 at 20:47
yes. First you load the first file as you already know how to do. That's done. Now you got a problem with the second file and those answers show you how to solve *that*. — mkrieger1, Jul 02 '21 at 20:49

fthomson · Accepted Answer · 2021-07-02T20:52:15.297

1

filename = open(sys.argv[1], "r")
Matriz = loadtxt(sys.argv[1], comments="#", delimiter=",", unpack=False)
filename.close()

filename = open(sys.argv[2], "r")
Atomos = loadtxt(sys.argv[2], comments="#", delimiter=",", unpack=False)
filename.close()
# change one of these to 2
# python test.py Matriz Atomos

If the text file is indentical to what was posted then change Atomos to

import pandas as pd
Atomos = pd.read_csv(sys.argv[2])

edited Jul 02 '21 at 20:52

answered Jul 02 '21 at 20:36

fthomson

773
3
9

I have updated my question, in it is the error posted – Another.Chemist Jul 02 '21 at 20:40
I guess python tried to created a numerical matrix but instead receive characters... I do not know how to process that error – Another.Chemist Jul 02 '21 at 20:41
you could just store it as a series/dataframe – fthomson Jul 02 '21 at 20:44

Read several files from command line

1 Answers1