Restriction_enzyme_count_complete

Restriction_enzyme_count_complete.py

import re
import sys
# DNA = input('Please enter your DNA sequence...').upper()
# while re.search('[^AGCT]', DNA):
#     DNA = input('Please enter a valid DNA sequence...').upper()

DNA = open('E.coli_genome.fasta').read()

pattern = sys.argv[1].upper()
pattern2 = sys.argv[2].upper()
count_no = int(sys.argv[3])

def restriction_enzyme_func(pattern, pattern2):
    result = []
    for m in re.finditer(pattern, DNA):
        result.append(m.group())

    for x in re.finditer(pattern2, DNA):
        result.append(x.group())

    return result

restriction_site_count = {}
for pat in restriction_enzyme_func(pattern, pattern2):
    current_count = restriction_site_count.get(pat, 0)
    new_count = current_count + 1
    restriction_site_count[pat] = new_count


for pattern, count in restriction_site_count.items():
    if count > count_no:
        print('The restriction enzyme site ' + pattern + ' is present : ' + str(count) + ' times')