How to write the lists of lists generated by this for loop to a file (Python)?

Question

I am having some trouble with getting the output lists from my one hot encoder to be written into a file. Here is the code showing how these lists are generated. The input files contain several DNA sequences which look like this, as an example:

>seq1
AGTAGATAG
>seq2
GGTTAACCG

This is the Python code:

import sys

path = sys.argv[1]
file = open(path, 'r')

holder = file.read()
holder1 = str(holder)
holder2 = holder1.replace("\n","")
uppercase = holder2.upper()

import re
test = re.sub('1|2|3|4|5|6|7|8|9|0|\t|SEQ|CHR|-|:', "", uppercase)
newone = test.split(">")
newone = [x for x in newone if x]

#checking for presence of N in sequence
lettern = "N"
result = [component for component in lettern if(component in newone)]

#if N is present in sequence, an error message is displayed

for line in newone:

    if (bool(result)) == True:
        print("The input sequence is invalid, N is present.")
        sys.exit()

#if sequence is in the correct format, proceed with one hot encoding

    else:   
     #mapping of bases to integers as a dictionary
        bases = "ATCG"
        base_to_integer = dict((i, c) for c, i in enumerate(bases))

    #encoding input sequence as integers

        integer_encoded = [base_to_integer[y] for y in line]      

    #one hot encoding
        onehot_encoded = list()
        for value in integer_encoded:
            base = [0 for x in range(len(bases))]
            base[value] = 1
            onehot_encoded.append(base)
        print(onehot_encoded)

I have tried amending the for loop at the end in many different ways, but I still cannot get it to write the whole output into one file, it usually ends up showing me the last encoded sequence only. This is the closest I got to a solution:

        onehot_encoded = list()
        temporal = list()
        for value in integer_encoded:
            base = [0 for x in range(len(bases))]
            base[value] = 1
            onehot_encoded.append(base)
        temporal.extend(onehot_encoded)

        with open("output", "a") as file:
            file.write(str(temporal))
        file.close()

However, this ends up repeating the loop, and also shows a very strange-looking jumble of my username and server name in the Linux after I run it and view the output file.

I would really appreciate any help with getting this whole output into one file.

Answer 1

It seems that your problem is, you are resetting the output structure inside the loop, so when you try to print to file only the last encoding is available.

I say seems because your code is quite complicated, in particular you keep recomputing things that can be put outside of the loop.

To emend your program ① put the stop condition outside of the loop, ② open the output file before starting the loop, ③ use a dictionary to precompute the encodings for the different bases ④ simplify the loop because we can do a dictionary lookup instead of recomputing the encoding every time and ⑤ print to the output file using the keyword argument file=...

stop_letters = "N"
for stop_letter in stop_letters:
    if stop_letter in newone : sys.exit()

out = open(..., 'w')
d = {"A":[1,0,0,0], "T":[0,1,0,0], "C":[0,0,1,0], "G":[0,0,0,1,]}

for bases in newone:
    onehot_encoded = [d[base] for base in bases]
    print(onehot_encoded, file=out)

out.close()