Splicing through a line of a textfile using python

Question

I am trying to create genetic signatures. I have a textfile full of DNA sequences. I want to read in each line from the text file. Then add 4mers which are 4 bases into a dictionary. For example: Sample sequence

ATGATATATCTATCAT

What I want to add is ATGA, TGAT, GATA, etc.. into a dictionary with ID's that just increment by 1 while adding the 4mers.

So the dictionary will hold...

Genetic signatures, ID
ATGA,1
TGAT, 2
GATA,3

Here is what I have so far...

import sys  

def main ():
    readingFile = open("signatures.txt", "r")
    my_DNA=""

    DNAseq = {} #creates dictionary 

    for char in readingFile:
        my_DNA = my_DNA+char

    for char in my_DNA:             
        index = 0
        DnaID=1
        seq = my_DNA[index:index+4]         

        if (DNAseq.has_key(seq)): #checks if the key is in the dictionary
            index= index +1
        else :
            DNAseq[seq] = DnaID
            index = index+1
            DnaID= DnaID+1

    readingFile.close()

if __name__ == '__main__':
    main()

Here is my output:

ACTC
ACTC
ACTC
ACTC
ACTC
ACTC

This output suggests that it is not iterating through each character in string... please help!

Answer 1

You need to move your index and DnaID declarations before the loop, otherwise they will be reset every loop iteration:

index = 0
DnaID=1
for char in my_DNA:             
    #... rest of loop here

Once you make that change you will have this output:

ATGA 1
TGAT 2
GATA 3
ATAT 4
TATA 5
ATAT 6
TATC 6
ATCT 7
TCTA 8
CTAT 9
TATC 10
ATCA 10
TCAT 11
CAT 12
AT 13
T 14

In order to avoid the last 3 items which are not the correct length you can modify your loop:

for i in range(len(my_DNA)-3):
    #... rest of loop here

This doesn't loop through the last 3 characters, making the output:

ATGA 1
TGAT 2
GATA 3
ATAT 4
TATA 5
ATAT 6
TATC 6
ATCT 7
TCTA 8
CTAT 9
TATC 10
ATCA 10
TCAT 11

Answer 2

This should give you the desired effect.

from collections import defaultdict

readingFile = open("signatures.txt", "r").read()
DNAseq      = defaultdict(int)
window      = 4

for i in xrange(len(readingFile)):
    current_4mer = readingFile[i:i+window]
    if len(current_4mer) == window:
        DNAseq[current_4mer] += 1

print DNAseq