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016. Finding a Protein Motif.py
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016. Finding a Protein Motif.py
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# There seems to be an error with some of the files being called because uniprot changes their names.
# Remove Names from the files in place of numbers
# For that reason I was unable to complete this problem, but left the code here for later attempts
import requests
import re
def read_uniprot_ids(file_path):
with open(file_path, 'r') as file:
fasta_data = file.readlines()
return fasta_data
def fetch_fasta_data(uniprot_id):
clean_id = uniprot_id.split('_')[0]
url = f"http://www.uniprot.org/uniprot/{clean_id}.fasta"
response = requests.get(url)
if response.status_code == 200:
fasta_data = response.text
sequence = ''.join(fasta_data.splitlines()[1:])
return sequence
else:
print(f"Error fetching data for {uniprot_id}: HTTP Status {response.status_code}")
return None
def find_motif_locations(sequence, motif_pattern):
return [m.start() + 1 for m in re.finditer(motif_pattern, sequence)]
def main(uniprot_ids):
motif_pattern = r'N[^P][ST][^P]'
results = {}
for uniprot_id in uniprot_ids:
sequence = fetch_fasta_data(uniprot_id)
if sequence:
locations = find_motif_locations(sequence, motif_pattern)
if locations:
results[uniprot_id] = locations
else:
print(f"No motifs found in {uniprot_id}")
else:
print(f"Failed to fetch sequence for {uniprot_id}")
return results
file_path = 'C:/Users/scien/Desktop/rosalind_mprt2.txt'
uniprot_ids = read_uniprot_ids(file_path)
result = main(uniprot_ids)
for uniprot_id, locations in result.items():
print(uniprot_id)
print(" ".join(map(str, locations)))