rosalind-solutions/python/MPRT.py

#!/usr/bin/python
# MPRT - Finding a Protein Motif Solution
# Problem can be found at http://rosalind.info/problems/mprt/
# Author: Peter Vlasveld

import re
from time import sleep

import requests

# declare motif
motif = "N[^P][ST][^P]"

# read in file
f0 = open("rosalind_mprt.txt", "r")
content = f0.read().splitlines()
f0.close()

# open output file
f1 = open("output.txt", "w+")
# loop through each accession ID
for i in content:
    # get fasta from url
    url = "http://www.uniprot.org/uniprot/" + i.split("_")[0] + ".fasta"
    response = requests.get(url)

    if response.status_code != 200:
        print(f"uniprot request failed for {i}")
        print(f"detail: {response.text}")

    fasta = response.text.splitlines()

    # format protein string
    protStr = ""
    for j in fasta:
        if not j.startswith(">"):
            protStr += j
    # construct output strings
    outStr = ""
    for j in range(0, len(protStr) - 4):
        if re.match(motif, protStr[j: j + 4]):
            outStr += str(j + 1) + " "

    # output
    if not outStr == "":
        print(i)
        f1.write(i + "\n")
        print(outStr)
        f1.write(outStr + "\n")

    sleep(1)
# close output file
f1.close()