solution1_list.py

#!/usr/bin/env python3
""" Compute GC content """

import argparse
import sys
from typing import NamedTuple, TextIO, List, Tuple
from Bio import SeqIO


class Args(NamedTuple):
    """ Command-line arguments """
    file: TextIO


# --------------------------------------------------
def get_args() -> Args:
    """ Get command-line arguments """

    parser = argparse.ArgumentParser(
        description='Compute GC content',
        formatter_class=argparse.ArgumentDefaultsHelpFormatter)

    parser.add_argument('file',
                        metavar='FILE',
                        type=argparse.FileType('rt'),
                        nargs='?',
                        default=sys.stdin,
                        help='Input sequence file')

    args = parser.parse_args()

    return Args(args.file)


# --------------------------------------------------
def main() -> None:
    """ Make a jazz noise here """

    args = get_args()
    seqs: List[Tuple[float, str]] = []

    for rec in SeqIO.parse(args.file, 'fasta'):
        # Iterate each base and compare to G or C, add 1 to counter
        gc = 0
        for base in rec.seq.upper():
            if base in ('C', 'G'):
                gc += 1
        pct = (gc * 100) / len(rec.seq)
        seqs.append((pct, rec.id))

    high = max(seqs)
    print(f'{high[1]} {high[0]:0.6f}')


# --------------------------------------------------
if __name__ == '__main__':
    main()