Can i save Two-Dimensional Arrays to text file in python

Question

How can I save a 2-dimensional array into a text file with python? I tried to do it as follows, but I get an error:

readcodon= open("codon.txt","r")
triplets=readcodon.read().split()
for i in range(0,len(triplets)):
   A=np.array(triplets, dtype=None)
readcodon.write(A)

This is the error message:

readcodon.write(A)

TypeError: write() argument must be str, not numpy.ndarray

Here is a sample of codon.txt:

TTT TCT TAT TGT TTC

The expected output in the file text:

[TTT, TCT, TAT, TGT, TTC ]

I edit it @yoonghm

kkx
– kkx

2021-02-15 22:50:18 +00:00
Commented Feb 15, 2021 at 22:50 — kkx
– kkx, Commented Feb 15, 2021 at 22:50
I edit it @yoonghm

kkx
– kkx

2021-02-15 23:04:57 +00:00
Commented Feb 15, 2021 at 23:04 — kkx
– kkx, Commented Feb 15, 2021 at 23:04

simonedimaria · Accepted Answer · 2021-02-15 23:09:03Z

2

For readability and simplicity, you can just use the numpuy.savetxt() function of numpy.

This method is used to save an array to a text file. This is an example of writing a 2d array into a file:

# Python program explaining 
# savetxt() function 
import numpy as geek 

x = geek.array([[1,2],[3,4]])
print("x is:") 
print(x) 

# X is an array 
c = geek.savetxt('geekfile.txt', x, delimiter =', ') 
a = open("geekfile.txt", 'r')# open file in read mode 

print("the file contains:") 
print(a.read())

Also, take a look at the official documentation, and at the geeksforgeeks numpuy.savetxt() guide for any doubts and clarifications.

answered Feb 15, 2021 at 23:09

simonedimaria

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1 Comment

kkx Over a year ago

thank you very much for your help @simonedimaria

Sash Sinha · Accepted Answer · 2021-02-15 23:32:28Z

Say you have a file codon.txt with the following contents:

TTT TCT TAT TGT TTC

I don't think you need to redudantly convert the list returned from split into a numpy array to achieve your desired output:

with open('codon.txt', 'r+') as codon_file:
    triplets = codon_file.read().split()
    codon_file.seek(0)
    codon_file.write(f"[{', '.join(triplets)}]")
    codon_file.truncate()

The contents of codon.txt after running above:

[TTT, TCT, TAT, TGT, TTC]

If you absolutely need the output to have the extra space after the last element of the list i.e:

[TTT, TCT, TAT, TGT, TTC ]

You can add the space before the end of the f-string:

codon_file.write(f"[{', '.join(triplets)} ]")
#                                        ^
#                                        |
#                                        space character

straeter · Accepted Answer · 2021-02-15 23:07:40Z

0

write() function wants a string. You can make a string out of your array or you can use numpys built-in write function instead:

np.savetxt(readcodon,A)

I think there is also a mistake in your for loop, it does three times the same thing, maybe you want to use your loop index i.

answered Feb 15, 2021 at 23:07

straeter

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