From vertical to horizontal output in python?

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I'm trying to create two lists of random dna sequences, dna1 and dna2. My code below is returning the random sequences of dna1 and dna2 in vertical order. I wonder how could I create a list for each dna result in horizontal format.

import numpy as np 
BASES = ('A','C','T','G')

def random_dna_sequence(length):
    return ''.join(np.random.choice(BASES,length)) #list() can be used 

with open('dna.txt', 'w+') as txtout:
    for _ in range(3):
        dna1 = random_dna_sequence(2)
        dna2 = random_dna_sequence(2)
        txtout.write(dna1)
        txtout.write(dna2)
        txtout.write("")
        print(dna1)
        print(dna2)

Output:

 CT
 AC
 AC

 AT
 AG
 CC

Expected outcome:

 dna1 = ['CT','AC','AC']
 dna2 = ['AT','AG','CC']
list python
2 Answers

Do you have to use the file? If you need lists, then the code will be like this.

import numpy as np 
BASES = ('A','C','T','G')

def random_dna_sequence(length):
    return ''.join(np.random.choice(BASES,length)) #list() can be used 

dna1 = [random_dna_sequence(2) for _ in range(3)]
dna2 = [random_dna_sequence(2) for _ in range(3)]

print(dna1)
print(dna2)

Returned values:

['AG', 'CG', 'AG']
['TA', 'TC', 'AA']
user_129930400

Александр Рахмаев answered with a working solution.

Just want to highlight your issue here.

Already working: from array to pairs

Seems in your domain (Genetics) you are combining bases (single letters from a specific set of 4) to pairs (string of 2 letters).

Therefore you use numpy's function to randomize the combination: np.random.choice(BASES, 2). It will return an array, try print( np.random.choice(BASES, 2) ), looks similar to:

array(['A', 'T']) # 1 dimensional array with 2 random elements

Now you need to combine these 2 elements to a pair, joined with empty-string '', which means concatenated to a String. So print( ''.join(np.random.choice(BASES,2)) ) will print

AT

You can now add many of these random pairs to a list. Your code did so using a for-loop with 3 iterations:

for _ in range(3):  # for each of the 3 iterations do:
    print( random_dna_sequence(2) )  # print each random base-pair

In fact the output is 3 separate lines.

The other answer did same 3 iterations shorter, inside the brackets ([], list-comprehension): random_dna_sequence(2) for _ in range(3)

Issue: add each pair to a list (data structure)

Then you can print the finally filled list after the 3rd element has been added. Python's print-function will then automatically format the list as you expected, almost:

['AG', 'CG', 'AG']

List comprehension (pythonic)

What the other answer accomplished with list-comprehension inside the brackets:

# add 3 random pairs to a list, named variable: dna
dna = [random_dna_sequence(2) for _ in range(3)]
  • create a list dna and add all 3 elements from iteration inside brackets
  • the right-hand side of the assigning = is called list-comprehension

For loop (generic)

Same can be done by your for-loop. All you need to change is:

  • define dna as an empty list before the loop
  • add the pair to the list, inside your loop (for each of the 3 iterations): dna.add( pair )
  • print the list named dna after the loop (code formatted without indentation)

Difficulty for beginners

I found a similar question: New to learning python; why is the print for this for-loop different when I use a list comprehension? how do i make the loop be the same?. This might shed light on some difficulties.

Solution: adding pairs to a list

The file-writing is omitted!

dna1 = []  # define empty list
dna2 = []

for _ in range(3):
    dna1.append( random_dna_sequence(2) )  # add pair to list
    dna2.append( random_dna_sequence(2) )

print(dna1)  # print list containing 3 elements (3 pairs)
print(dna2)

Now, to add something in front, simply add inside the print-function - separated by comma: print('dna2 =', dna2) will output as expected

dna1 = ['AG', 'CG', 'AG']

For the file-output the question remains:

  • How do you expect the contents (here: the pairs) to be written?
    • A pair per line
    • All pairs in one line, maybe separated by comma or enclosed in quotes.
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