Extract, filter and match three letters from the given arguments and predict the name

Question

Case 1: rank1_naming

This function takes two arguments

• list_proteins_pattern_available
• best_match_protein_name

Objective: Extract the three letter pattern from the both arguments. Match the pattern and keep only the matched items. Extract the numbers from list_proteins_pattern_available and also sort it. Find the maximum number from the collected numbers and add 1 to get the next number.

Please let me know if you have any questions.

Can you point ways to improve this script?

import re
def case_rank1_naming(list_proteins_pattern_available, best_match_protein_name):
 #This will store the list of numbers
 available_list_numbers = []
 #extract the three letter pattern
 protein_pattern = re.search(r"[A-Z]{1}[a-z]{2}", best_match_protein_name)
 protein_pattern = protein_pattern.group()
 #extract the numbers
 for name in list_proteins_pattern_available:
 pattern = re.search(r"[A-Z]{1}[a-z]{2}\d{1,3}", name)
 number = re.search(r"\d{1,3}", pattern.group())
 available_list_numbers.append(number.group())
 #Convert all the string numbers to integers
 available_list_numbers = [int(x) for x in available_list_numbers]
 #Sort the available number. Just realized I use two times sort function.
 available_list_numbers.sort()
 # Sort the available number, get the maximum number and add one to get next number
 # Example: result will be 50
 primary_number_prediction = int(max(sorted(available_list_numbers))) + 1
 #Add the protein pattern, the next predicted number and 'Aa1' at the suffix
 predicted_name = protein_pattern + str(primary_number_prediction) + 'Aa1'
 return predicted_name
list_proteins_pattern_available = ['Xpp1Aa1', 'Xpp2Aa1', 'Xpp35Aa1', 'Xpp35Ab1', 'Xpp35Ac1', 'Xpp35Ba1', 'Xpp36Aa1', 'Xpp49Aa1', 'Xpp49Ab1']
best_match_protein_name = 'Xpp35Ba1'
predicted_name = case_rank1_naming(list_proteins_pattern_available, best_match_protein_name)
print(predicted_name)
#Xpp50Aa1

Answer 1

I'll show an example implementation first, and then describe it:

from typing import Iterable
import re
def case_rank1_naming(proteins_available: Iterable[str], best_match_protein_name: str) -> str:
 # extract the three-letter pattern
 protein_pattern = re.search(r"[A-Z][a-z]{2}", best_match_protein_name).group()
 # extract the numbers
 best_number = max(
 int(re.search(r"[A-Z][a-z]{2}(\d{1,3})", name)[1])
 for name in proteins_available
 )
 # Add the protein pattern, the next predicted number and 'Aa1' at the suffix
 return f'{protein_pattern}{best_number + 1}Aa1'
def main():
 proteins_available = (
 'Xpp1Aa1', 'Xpp2Aa1', 'Xpp35Aa1', 'Xpp35Ab1', 'Xpp35Ac1',
 'Xpp35Ba1', 'Xpp36Aa1', 'Xpp49Aa1', 'Xpp49Ab1'
 )
 best_match_protein_name = 'Xpp35Ba1'
 predicted_name = case_rank1_naming(proteins_available, best_match_protein_name)
 assert predicted_name == 'Xpp50Aa1'
if __name__ == '__main__':
 main()

• Add type hints to better-define your function signature
• Don't write {1} in a regex - you can just drop it
• Call max immediately on a generator rather than making and sorting a list
• Shorten your variable names. Especially don't include the type of the variable in its name. Type hints and appropriate pluralization will cover you instead.
• Use f-strings
• Have a main function
• In main, use a tuple for proteins_available instead of a list because it doesn't need to mutate

• dfhwze: you are on a roll :)
• catuf: Thank you. I will go through it and understand.
• catuf: Why this step assert predicted_name == 'Xpp50Aa1'. In many cases we don't know the predicted name. right? Is this for testing?
• Reinderien: Yes, it's only for testing. You'll definitely want to leave that out in general program use, and move it to a unit test.