Converting nucleotides to the corresponding DNA sequence

Question

I´m working on an assignment in python. I have to find a function or a program that converts this list to the corresponding DNA sequence.

bases_list = ['Adenosine', 'Guanine', 'Thymine', 'Cytosine', 'Thymine', 'Adenosine', 'Guanine', 'Cytosine', 'Thymine', 'Adenosine', 'Guanine']

print(dna)

AGTCTAGCTAG  #the output

I think maybe I can make a definition function to convert those bases to corresponding letters. How can I do that? Any ideas?

PS: I began to learn python very recently, so I hope you guys can help me :)

But I have to print as print(dna), which means that I have to find a function that I should call as "dna". Do you think I have to write a def function? — strawberrrry, Oct 31 '17 at 13:00
I think you need to learn the basics of Python programming first. — Mike Scotty, Oct 31 '17 at 13:01

score 4 · Answer 1 · answered Oct 31 '17 at 13:02

Yes a few! as you begin not a long time ago, let do something simple:

bases_list = ['Adenosine', 'Guanine', 'Thymine', 'Cytosine', 'Thymine', 'Adenosine', 'Guanine', 'Cytosine', 'Thymine', 'Adenosine', 'Guanine']

dna = "" # You begin with the dna empty

for sequence in bases_list: # you go throw every chain
  dna += sequence[0] # you add the first letter with the op [0] of lists

print(dna) # finally print

You can read about the basis of loop here https://wiki.python.org/moin/ForLoop

score 2 · Answer 2 · answered Oct 31 '17 at 12:58

2

Most succinct:

print("".join([x[0] for x in bases_list]))

dna = "".join(x[0] for x in bases_list])
print(dna)

otherwise:

dna = ""
for base in bases_list:
    dna += base[0] . # get 1st letter from base
print(dna)

answered Oct 31 '17 at 12:58

Daniel Lee

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score 2 · Answer 3 · answered Oct 31 '17 at 13:01

2

Let's use string indexing and join:

dna = ''.join(i[0] for i in bases_list)
print(dna)

Output:

AGTCTAGCTAG

answered Oct 31 '17 at 13:01

Scott Boston

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What does the join syntax actually? I never saw that in our course :) – strawberrrry Oct 31 '17 at 13:02
@berr Join takes each element from an iterable and concatenates them into one string with or with a separator. [See docs](https://docs.python.org/3.6/library/stdtypes.html#str.join) – Scott Boston Oct 31 '17 at 13:04

cs95 · Answer 4 · 2017-10-31T13:05:23.110

2

How about a map?

In [276]: ''.join(map(lambda x: x[0], bases_list))
Out[276]: 'AGTCTAGCTAG'

str.join is used to take a list (or any iterable) of strings and join them together. map applies the same function to every element in an iterable.

Quick note. I ran this code on a terminal, but if you're running this in a script, don't forget to assign the result back to another variable.

seq = ''.join(map(lambda x: x[0], bases_list))
print(seq)

edited Oct 31 '17 at 13:05

answered Oct 31 '17 at 13:02

cs95

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Nice one, for advanced users ;) I'm thinking another simple way but I don't came with Ideas, do you have any else? – developer_hatch Oct 31 '17 at 13:05
@DamianLattenero No, I believe every simple option has been discussed in these answers. Anything else will need some thinking :) – cs95 Oct 31 '17 at 13:06

score 0 · Answer 5 · answered Oct 31 '17 at 13:40

For completeness I thought I would add the itemgetter https://docs.python.org/3/library/operator.html#operator.itemgetter solution.

In this case, it gets the character in index (0) of every element in bases_list. It is said to be slightly faster and cleaner than lambda operator.itemgetter or lambda

from operator import itemgetter

bases_list = ['Adenosine', 'Guanine', 'Thymine', 'Cytosine', 'Thymine',
              'Adenosine', 'Guanine', 'Cytosine', 'Thymine', 'Adenosine', 'Guanine']
dna = "".join((map(itemgetter(0),bases_list)))

print (dna)

result:

AGTCTAGCTAG

score 0 · Answer 6 · answered Nov 02 '17 at 14:37

If you want a function that converts the base name to its corresponding letter, you are lucky here, because it is simply the first letter of the base name.

Taking the first letter of a string is easily done by "indexing". For instance:

base = "Adenosine"
letter = base[0]
# letter should now be "A"

In a simple case like this, one would probably not bother defining a specific function, but it is possible and may look as follows:

def base2letter(base):
    """This function converts the name of a base into the corresponding letter."""
    return base[0]

Now you can apply the function to every base name in your list. The usual way to do this in python is by using a "list comprehension":

letters_list = [base2letter(base) for base in bases_list]

What you have now is the list of the letters: ["A", "G", "T", "C", "T", "A", "G", "C", "T", "A", "G"]

The next step is to join them together into a string. An efficient way to do this is to use the join method that is defined for strings. It sticks the string between the successive elements it is given: "_".join(["A", "B", "C"]) will result in "A_B_C". Here you want to put the letters together with nothing between them, so you have to use the empty string:

dna = "".join(letters_list)

Note that progressively building the string in a for loop by concatenating new letters one by one to the current state of the string is possible (see https://stackoverflow.com/a/47036161/1878788). This may be expected of you if python is just used to give you a general idea of how programming languages using an "imperative" style work. However, it is not efficient in python, that is why many answers did not use this technique.

Converting nucleotides to the corresponding DNA sequence

6 Answers6