Program without module

user_10451917 0
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I have the following program:

from collections import Counter
counter=0
lst=list()
fhandle=open('DNAInput.txt','r')
for line in fhandle:
    if line.startswith('>'):
       continue
    else:
       lst.append(line)
while counter != len(lst[0]):
    lst2=list()
    for word in lst:
        lst2.append(word[counter])
    for letter in lst2:
        mc=Counter(lst).most_common(5)
    counter=counter +1
    print(mc)

which takes the following inout file:

>1
GATCA
>2
AATC
>3
AATA
>4
ACTA

And prints out the letter that repeats the most in each Collin. How can I make the exact same file without the "from collections import Counter"

python-2.7 python-3.x python
2 Answers

If I understand what you are trying to do; find the most common character in each column(?) here is how you can do it:

def most_common(col, exclude_char='N'):
    col = list(filter((exclude_char).__ne__, col))
    return max(set(col), key=col.count)

sequences = []
with open('DNAinput.txt', 'r') as file:
    for line in file:
        if line[0] == '>':
            continue
        else:
            sequences.append(line.strip())

m = max([len(v) for v in sequences])
matrix = [list(v) for v in sequences]
for seq in matrix:
    seq.extend(list('N' * (m - len(seq))))
transposed_matrix = [[matrix[j][i] for j in range(len(matrix))] for i in range(m)] 

for column in transposed_matrix:
    print(most_common(column))

This works by:

Opening your file and reading it into a list like this:

# This is the `sequences` list
['GATCA', 'AATC', 'AATA', 'ACTA']

Get the length of the longest DNA sequence:

# m = max([len(v) for v in sequences])
5

Create a matrix (list of lists) from these sequences:

# matrix = [list(v) for v in sequences]
[['G', 'A', 'T', 'C', 'A'],
 ['A', 'A', 'T', 'C'],
 ['A', 'A', 'T', 'A'],
 ['A', 'C', 'T', 'A']]

Pad the matrix so all the sequences are the same length:

# for seq in matrix:
#     seq.extend(list('N' * (m - len(seq))))
[['G', 'A', 'T', 'C', 'A'],
 ['A', 'A', 'T', 'C', 'N'],
 ['A', 'A', 'T', 'A', 'N'],
 ['A', 'C', 'T', 'A', 'N']]

Transpose the matrix so columns go top -> bottom (not left -> right). This places all the characters from the same position into a list together.

# [[matrix[j][i] for j in range(len(matrix))] for i in range(m)]
[['G', 'A', 'A', 'A'],
 ['A', 'A', 'A', 'C'],
 ['T', 'T', 'T', 'T'],
 ['C', 'C', 'A', 'A'],
 ['A', 'N', 'N', 'N']]

Finally, iterate over each list in the transposed matrix and call most_common with the sub-list as input:

# for column in transposed_matrix:
#     print(most_common(column))
A
A
T
C
A

There are caveats to this approach; firstly, the most_common function I have included will return the first value in the event that there are the same number of nucleotides in a single postion (see position four, this could have been either A or C). Furthermore, the most_common function could take exponentially more time than using Counter from collections.

For these reasons, I would strongly recommend using the following script instead as collections is included with python on installation.

from collections import Counter

sequences = []
with open('DNAinput.txt', 'r') as file:
    for line in file:
        if line[0] == '>':
            continue
        else:
            sequences.append(line.strip())

m = max([len(v) for v in sequences])
matrix = [list(v) for v in sequences]
for seq in matrix:
    seq.extend(list('N' * (m - len(seq))))
transposed_matrix = [[matrix[j][i] for j in range(len(matrix))] for i in range(m)] 

for column in transposed_matrix:
    print(Counter(column).most_common(5))
user_32797160

You would have to go to the Collections module, in my case is located here:

C:\Python27\Lib\collections.py

And grab the parts you need and copy them into your script, in your case you need the Counter class.

This could get complicated if the Counter class is sourcing other things from that's script or other imported modules. You could go to those imported modules and also copy the code into your script but they as well could be referencing more modules.

What is the reason why you don't want to import a module in your script? Maybe there is a better solution to your problem than not importing anything.

user_55790110
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