protein_motif_search.py

#!/usr/bin/env python

""" Finding all occurrences of N-glycosylation motif in a protein"""

__author__ = "Navami Shenoy"

import requests

def fetchFASTA(protein_id):
    """ gets the protein sequence from the FASTA file
        of a given protein using its access ID """
    url = 'https://www.uniprot.org/uniprot/'
    data = requests.get(url+protein_id+".fasta") # retrieve FASTA file
    sequence = data.text.split('\n') # get sequence from the file
    return "".join(sequence[1:])

def n_gly_motif_search(protein_id):
    """ find all positions in the protein sequence
        where the N-glycosylation motif occurs """
    sequence = fetchFASTA(protein_id)
    positions = []

    for i in range(0, len(sequence)-3):
        if sequence[i] == 'N' and sequence[i+1] != 'P' and sequence[i+3] != 'P':
            if sequence[i+2] == 'S' or sequence[i+2] == 'T':
                positions.append(i+1)
    
    return protein_id, positions
    

# testing 
protein_id, positions = n_gly_motif_search('B5ZC00')
print(protein_id)
print(*positions)
# Output: B5ZC00     
#         85 118 142 306 395     

# testing
with open('rosalind_mprt.txt') as f: # Test file source: www.rosalind.info 
    protein_IDs = f.read().split("\n")
    for ID in protein_IDs:
        protein_id, positions = n_gly_motif_search(ID)
        # return positions only if the motif exists:
        if len(positions) != 0: 
            print(protein_id)
            print(*positions)