so i m a bit confused...i have been testing my code using the small database and what i have so far produced what i expected .... more specifically the STRcounts (i marked that part #?????). it is supposed to find the STR patterns (given in the dictionary) in the dna sequence ...and the numbers match when i test the small database but when i use the large one the counts don`t match ....i think the code is logical unless i misunderstood the .findall() function...? any clarifications would be much appreciated

import sys
import csv
import re

# promp for command line arguments
if len(sys.argv) != 3:
    print("Usage: python dna.py data.csv sequence.txt")

# open sequence (txt file) and save its contents into memory
with open(sys.argv[2], "r") as seq:
    dna_seq = seq.read()

# get a list of the STRs in the file
with open(sys.argv[1], "r") as f:
    reader = csv.reader(f)
    STRs = next(reader)

# calculate the repetions of each STR given in the csv file(in the header)
STRcounts = []
for i in range(1, len(STRs)):
    x = re.findall(STRs[i], dna_seq)    #???????????
with open(sys.argv[1], "r") as file:
    #calculate the number of rows in the database
    row_count = sum(1 for row in file)

results = {}
# insert strs and their count into the dictionary
for i in range(len(STRcounts)):
    results[STRs[i + 1]] = STRcounts[i]

1 Answer 1


oh well..i was dumb...the STRs have to repeat next to each other ... re.findall() just returns all of them no matter where they are in the sequence ...

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