Function that find the ATP binding site

Question

[nessrineN]

Hello ,

I'm currently doing a python project where I need a code that extract the ATP binding site from a FASTA file thanks to an regular expression more precisely a pattern.

Thanks for your help :)

Ps: Look at what I already did

[WouterDeCoster]

What's the question? What have you tried?

[nessrineN]

I've tried this code but it does not work. It opens a new file but the file is empty. I don't know what's wrong.

from Bio import SeqIO
import re
import os
path="C:/Users/nessr/Desktop/info projet"
os.chdir(path)
records=list(SeqIO.parse("plasmo.fasta","fasta"))
ATPM="[LIV]G[^P]G[^P][FYWMGSTNH][SGA][^PW][LIVCAT][^PD].[GSTACLIVMFY].{5,18}[LIVMFYWCSTAR][AIVP][LIVMFAGCKR]K"
patern=re.compile(r"(ATPM)")

def atp_binding(records,patern):

    for item in records:
        for m in patern.findall(str(item)):
            istart=m.start()
            iend=m.end()

            iend=iend+50

            print(istart,m.group())


file = open("output.txt","w")

for seq_record in SeqIO.parse(records, "fasta"): 
    file.write(atp_binding(seq_record.records,patern)+"\n")
    file.write('-------------------\n')
file.close()