Extract DGE tag data from oriented fasta files. By default looks for CATG prefix and prints the 21 characters following it

DGE tag extract

#!/usr/bin/env python3
import re
import argparse

# Argument Parser
parser = argparse.ArgumentParser(description='Finds DGE tags from a multifasta')
parser.add_argument('-site',nargs="?",const="CATG",default="CATG",help='site the enzyme cuts at, by default CATG')
parser.add_argument('-length',nargs="?",type=int,const=21,default=21,help='length of tag to find, by default 21')
parser.add_argument('file', type=argparse.FileType('r'))
args = parser.parse_args()


# define function to invert DNA sequences
def my_reverse_complement(seq):
    return Seq(seq).reverse_complement()


enzyme_site = args.site
k_length = args.length
multifasta_file = args.file

# Make Regex that'll detect the tags
regex_length = args.length - len(enzyme_site)
regex_forward = r"" + enzyme_site + "[ATCG]{" + str(regex_length) +"}"

multifasta_file = multifasta_file.read()
fasta_seqs = multifasta_file.split(">")

for seq in fasta_seqs:
    header = seq.split("\n")[0]
    header = header.strip()
    seq = "".join(seq.split("\n")[1:])
    seq = seq.rstrip()
    print(">" + header)
    forward_matches = re.finditer(regex_forward, seq, re.MULTILINE)
    for matchNum, match in enumerate(forward_matches):
        matchNum = matchNum + 1
        print(match.group())
        print(match.group())