[Biopython/ChatGPT]アミノ酸配列を所定のGC含量に近いDNA配列へ逆翻訳する

ChatGPT (GPT-4) にBiopythonを使ったスクリプトを書かせる試みとして、タンパク質をDNAに逆翻訳するプログラムを書かせた。
どうにか動くスクリプトを完成させることができたが、プロンプトの書き方にコツがあるようだ。
要件定義をしっかりすることが重要だと再認識した。

back_translate_proteins.py

#!/usr/bin/env python

import argparse
import sys
import os
from Bio import SeqIO, Seq
from Bio.Data import CodonTable
import tqdm
import logging

logging.basicConfig(level=logging.INFO, stream=sys.stderr)

def calculate_gc_content(sequence):
    """Compute the GC content of a given sequence."""
    return (sequence.count('G') + sequence.count('C')) / max(1, len(sequence))


def heuristic_back_translate(sequence, protein_to_codon, desired_gc):
    nucleotide_seq = ""

    for aa in sequence:
        if aa not in protein_to_codon:
            continue

        current_gc = calculate_gc_content(nucleotide_seq)
        codons = sorted(protein_to_codon[aa], key=calculate_gc_content)

        if current_gc < desired_gc:
            nucleotide_seq += codons[-1]
        else:
            nucleotide_seq += codons[0]

    resulting_gc = calculate_gc_content(nucleotide_seq)
    return nucleotide_seq, resulting_gc
    
def calculate_min_max_gc(sequence, protein_to_codon):
    min_gc_seq = ''.join(sorted(protein_to_codon[aa], key=calculate_gc_content)[0] for aa in sequence if aa in protein_to_codon)
    max_gc_seq = ''.join(sorted(protein_to_codon[aa], key=calculate_gc_content, reverse=True)[0] for aa in sequence if aa in protein_to_codon)

    return calculate_gc_content(min_gc_seq), calculate_gc_content(max_gc_seq)

def process_record(record, protein_to_codon, desired_gc, file_format, output_file, gc_adjusted_count, tsv_report):
    min_gc, max_gc = calculate_min_max_gc(str(record.seq), protein_to_codon)
    current_desired_gc = desired_gc
    note = ""

    if current_desired_gc < min_gc:
        current_desired_gc = min_gc
        note = "desired GC% unreachable; adjusted to theoretical min"
        gc_adjusted_count[0] += 1
    elif current_desired_gc > max_gc:
        current_desired_gc = max_gc
        note = "desired GC% unreachable; adjusted to theoretical max"
        gc_adjusted_count[0] += 1

    translated_seq, resulting_gc = heuristic_back_translate(str(record.seq), protein_to_codon, current_desired_gc)

    record.seq = Seq.Seq(translated_seq)
    record.description += f" | Resulting GC: {resulting_gc*100:.2f}%"

    with open(output_file, 'a') as outfile:
        SeqIO.write(record, outfile, file_format)

    tsv_report.append([record.id, len(record.seq), min_gc * 100, max_gc * 100, resulting_gc * 100, note])

    return min_gc, max_gc, resulting_gc

def main(input_file, output_file, file_format, genetic_table_id, desired_gc, report_file):
    table = CodonTable.unambiguous_dna_by_id[genetic_table_id]
    protein_to_codon = {value: [key for key in table.forward_table if table.forward_table[key] == value] for value in table.forward_table.values()}

    sum_min_gc = 0
    sum_max_gc = 0
    sum_actual_gc = 0
    total_proteins = 0
    gc_adjusted_count = [0]
    tsv_report = []

    records = list(SeqIO.parse(input_file, file_format))

    for record in tqdm.tqdm(records, desc="Processing records"):
        min_gc, max_gc, actual_gc = process_record(record, protein_to_codon, desired_gc/100, file_format, output_file, gc_adjusted_count, tsv_report)

        sum_min_gc += min_gc
        sum_max_gc += max_gc
        sum_actual_gc += actual_gc
        total_proteins += 1

    avg_min_gc = (sum_min_gc / total_proteins) * 100
    avg_max_gc = (sum_max_gc / total_proteins) * 100
    avg_actual_gc = (sum_actual_gc / total_proteins) * 100

    logging.info(f"Summary:\nTotal proteins back translated: {total_proteins}\nAverage theoretical minimum GC: {avg_min_gc:.2f}%\nAverage theoretical maximum GC: {avg_max_gc:.2f}%\nAverage actual GC% of the backtranslated sequences: {avg_actual_gc:.2f}%")

    if gc_adjusted_count[0] > 0:
        percentage = (gc_adjusted_count[0] / total_proteins) * 100
        logging.warning(f"{gc_adjusted_count[0]} sequences ({percentage:.2f}%) were adjusted to fit the theoretical GC bounds.")

    with open(report_file, 'w') as rpt_file:
        rpt_file.write("id\tlength\ttheoretical_min_gc\ttheoretical_max_gc\tactual_gc\tnote\n")
        for line in tsv_report:
            rpt_file.write('\t'.join(map(str, line)) + '\n')

if __name__ == "__main__":
    default_output_name = None
    default_report_name = None
    parser = argparse.ArgumentParser(description="Back-translate protein sequences into nucleotide sequences.")
    parser.add_argument('-o', '--output', default=default_output_name, help=f'Output nucleotide sequence file. Default: {default_output_name}')
    parser.add_argument('-f', '--format', default="fasta", help='File format (default: fasta).')
    parser.add_argument('-t', '--table', type=int, default=1, help='Genetic table ID (default: 1).')
    parser.add_argument('--gc', type=float, default=50, help='Desired GC content (default: 50%%).')
    parser.add_argument('-r', '--report', default=default_report_name, help=f'Report file in TSV format detailing backtranslation results. Default: {default_report_name}')
    parser.add_argument('-i', '--input', required=True, help='Input protein sequence file.')
    args, _ = parser.parse_known_args()
    if args.input:
        base_name = os.path.splitext(os.path.basename(args.input))[0]
        default_output_name = f"{base_name}.fna"
        default_report_name = f"{base_name}_report.tsv"
        parser.set_defaults(output=default_output_name, report=default_report_name)
    if args.output:
        base_name = os.path.splitext(os.path.basename(args.output))[0]
        default_report_name = f"{base_name}_report.tsv"
        parser.set_defaults(report=default_report_name)
    args = parser.parse_args()

    main(args.input, args.output, args.format, args.table, args.gc, args.report)

$ ./back_translate_proteins.py -h
usage: back_translate_proteins.py [-h] [-o OUTPUT] [-f FORMAT] [-t TABLE] [--gc GC] [-r REPORT] -i INPUT

Back-translate protein sequences into nucleotide sequences.

optional arguments:
  -h, --help            show this help message and exit
  -o OUTPUT, --output OUTPUT
                        Output nucleotide sequence file. Default: None
  -f FORMAT, --format FORMAT
                        File format (default: fasta).
  -t TABLE, --table TABLE
                        Genetic table ID (default: 1).
  --gc GC               Desired GC content (default: 50%).
  -r REPORT, --report REPORT
                        Report file in TSV format detailing backtranslation results. Default: None
  -i INPUT, --input INPUT
                        Input protein sequence file.

$ ./back_translate_proteins.py -i GCF_000005845.2_ASM584v2_protein.faa -o GCF_000005845.2_ASM584v2_protein.gc55.fna -t 11 --gc 55
Processing records: 100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 4298/4298 [00:16<00:00, 260.77it/s]
INFO:root:Summary:
Total proteins back translated: 4298
Average theoretical minimum GC: 30.01%
Average theoretical maximum GC: 67.23%
Average actual GC% of the backtranslated sequences: 54.86%
WARNING:root:37 sequences (0.86%) were adjusted to fit the theoretical GC bounds

$ ./back_translate_proteins.py -i GCF_000005845.2_ASM584v2_protein.faa -o GCF_000005845.2_ASM584v2_protein.gc45.fna -t 11 --gc 45
Processing records: 100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 4298/4298 [00:15<00:00, 283.89it/s]
INFO:root:Summary:
Total proteins back translated: 4298
Average theoretical minimum GC: 30.01%
Average theoretical maximum GC: 67.23%
Average actual GC% of the backtranslated sequences: 45.04%

$ ./back_translate_proteins.py -i GCF_000005845.2_ASM584v2_protein.faa -o GCF_000005845.2_ASM584v2_protein.gc35.fna -t 11 --gc 35
Processing records: 100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 4298/4298 [00:14<00:00, 298.23it/s]
INFO:root:Summary:
Total proteins back translated: 4298
Average theoretical minimum GC: 30.01%
Average theoretical maximum GC: 67.23%
Average actual GC% of the backtranslated sequences: 35.34%
WARNING:root:77 sequences (1.79%) were adjusted to fit the theoretical GC bounds.

GCF_000005845.2_ASM584v2_protein.gc55.fna

>NP_414542.1 thr operon leader peptide [Escherichia coli str. K-12 substr. MG1655] | Resulting GC: 57.14%
ATGAAGCGGATTAGCACGACGATCACGACGACGATCACGATCACGACGGGGAATGGGGCT
GGT
>NP_414543.1 fused aspartate kinase/homoserine dehydrogenase 1 [Escherichia coli str. K-12 substr. MG1655] | Resulting GC: 55.00%
ATGCGGGTTTTAAAGTTCGGGGGGACGTCTGTGGCGAATGCGGAAAGATTCCTGCGGGTT
GCTGATATCCTGGAGAGCAATGCGCGGCAAGGTCAAGTTGCGACTGTTCTGAGCGCTCCT
GCTAAAATCACGAACCACCTGGTGGCGATGATTGAGAAGACGATCAGCGGGCAGGATGCG
TTACCGAATATCAGCGACGCGGAACGGATTTTCGCGGAACTGCTGACTGGGTTAGCGGCT
GCTCAACCTGGTTTTCCGTTAGCGCAATTAAAGACGTTCGTGGACCAGGAGTTCGCGCAG
ATTAAGCACGTGCTGCACGGGATTAGCCTGCTGGGGCAATGTCCGGATTCTATCAACGCG
GCTTTAATCTGCCGGGGGGAAAAAATGAGCATCGCGATCATGGCGGGGGTTCTGGAAGCG
AGAGGTCATAATGTGACGGTGATCGACCCGGTTGAGAAACTGCTGGCGGTTGGGCATTAT
CTGGAGAGCACTGTGGACATTGCGGAGTCTACGCGGAGAATTGCGGCTTCTCGGATTCCG
GCTGATCATATGGTGCTGATGGCGGGTTTTACGGCGGGTAATGAGAAAGGGGAGTTAGTG
GTGCTGGGGAGAAATGGGTCTGACTACAGCGCGGCTGTTTTAGCGGCTTGTCTGAGAGCG
GATTGTTGCGAAATCTGGACGGACGTGGATGGGGTTTATACGTGCGACCCGAGACAAGTG
CCTGATGCGAGATTACTGAAGAGCATGAGCTACCAGGAGGCGATGGAGCTGAGCTATTTC
GGGGCGAAAGTGCTGCACCCTAGAACGATTACGCCGATTGCGCAGTTTCAGATCCCGTGC
TTAATCAAGAACACGGGGAACCCGCAGGCGCCTGGTACTTTAATCGGGGCGTCTAGAGAC
GAAGACGAGTTACCGGTGAAAGGGATCAGCAACCTGAACAACATGGCGATGTTCAGCGTG
AGCGGGCCGGGTATGAAAGGGATGGTGGGTATGGCGGCTAGAGTTTTTGCGGCGATGTCT
AGAGCGAGAATTAGCGTGGTGCTGATCACGCAGAGCTCTAGCGAGTATAGCATCAGCTTC
TGCGTGCCGCAAAGCGACTGTGTGCGGGCTGAAAGAGCTATGCAGGAAGAGTTCTACCTG
GAGCTGAAGGAGGGGTTACTGGAGCCGTTAGCGGTTACTGAGCGGTTAGCGATTATCAGC
GTGGTGGGGGATGGTATGAGAACGCTGAGAGGGATTAGCGCGAAATTCTTCGCGGCGTTA
GCGAGAGCGAATATCAACATCGTGGCGATCGCGCAGGGTTCTAGCGAACGGTCTATTAGC
GTGGTGGTGAATAACGACGACGCGACGACTGGGGTTAGAGTGACGCATCAGATGCTGTTC
AACACGGACCAGGTGATCGAGGTGTTCGTGATCGGGGTTGGGGGTGTTGGTGGTGCTTTA
TTAGAGCAGCTGAAGCGGCAACAGAGCTGGTTAAAGAACAAGCACATCGACCTGCGGGTG
TGCGGGGTTGCTAATAGCAAGGCGCTGTTAACGAACGTGCACGGGTTAAACCTGGAGAAC
TGGCAGGAGGAGCTGGCGCAAGCTAAAGAGCCGTTTAACCTGGGGAGACTGATCCGGTTA
GTGAAGGAGTACCACCTGCTGAACCCGGTTATCGTGGACTGCACGTCTAGCCAGGCTGTT
GCTGATCAGTATGCGGACTTTCTGCGGGAAGGGTTTCACGTGGTGACTCCGAATAAGAAG
GCGAACACGAGCAGCATGGACTACTACCACCAGCTGCGGTATGCGGCTGAAAAGAGCCGG
AGAAAATTCCTGTACGACACGAACGTGGGGGCGGGTTTACCGGTTATTGAGAACCTGCAG
AACCTGCTGAACGCGGGGGATGAACTGATGAAGTTCAGCGGGATCCTGAGCGGGTCTTTA
AGCTACATCTTCGGGAAGCTGGACGAGGGGATGAGCTTTAGCGAGGCGACTACGTTAGCG
AGAGAGATGGGGTATACGGAGCCGGATCCTAGAGACGATCTGAGCGGTATGGACGTTGCG
AGAAAACTGCTGATCCTGGCGAGAGAGACTGGGAGAGAACTGGAGTTAGCGGACATTGAG
ATCGAGCCGGTTCTGCCGGCTGAATTTAACGCGGAGGGTGATGTGGCTGCTTTTATGGCG
AATCTGAGCCAGCTGGACGATCTGTTCGCGGCTAGAGTTGCGAAAGCGAGAGACGAAGGG
AAAGTGCTGAGATACGTGGGGAATATCGACGAGGACGGGGTTTGCAGAGTGAAGATCGCG
GAAGTGGACGGTAATGACCCGTTATTCAAGGTGAAGAACGGGGAGAACGCGCTGGCGTTT
TACAGCCACTACTACCAGCCGCTGCCGTTAGTGCTGAGAGGGTATGGGGCTGGTAATGAC
GTTACGGCGGCTGGTGTTTTTGCGGATTTACTGCGGACTCTGAGCTGGAAACTGGGGGTT
...

GCF_000005845.2_ASM584v2_protein.gc45.fna

>NP_414542.1 thr operon leader peptide [Escherichia coli str. K-12 substr. MG1655] | Resulting GC: 49.21%
ATGAAGCGGATTAGCACTACGATTACGACGACTATTACGATCACGACGGGTAATGGGGCT
GGT
>NP_414543.1 fused aspartate kinase/homoserine dehydrogenase 1 [Escherichia coli str. K-12 substr. MG1655] | Resulting GC: 45.04%
ATGCGGGTTTTAAAGTTCGGGGGTACTTCTGTTGCTAATGCGGAAAGATTTCTGCGGGTT
GCTGATATTCTGGAATCTAACGCGAGACAAGGTCAAGTTGCTACTGTTTTAAGCGCGCCT
GCTAAAATTACGAATCACCTGGTTGCTATGATTGAGAAGACGATTAGCGGGCAAGATGCT
TTACCGAATATCAGCGATGCGGAAAGAATTTTCGCGGAATTACTGACGGGTTTAGCGGCT
GCTCAACCTGGTTTTCCTTTAGCTCAATTAAAAACGTTCGTGGATCAGGAATTTGCGCAA
ATTAAGCACGTGCTGCATGGGATTTCTCTGTTAGGGCAATGTCCTGATTCTATTAACGCG
GCTTTAATCTGCCGGGGTGAAAAAATGAGCATTGCGATTATGGCGGGTGTTTTAGAGGCT
AGAGGTCATAATGTGACTGTGATTGACCCGGTTGAAAAACTGTTAGCGGTTGGTCATTAT
CTGGAGTCTACGGTTGATATCGCGGAATCTACTAGACGGATTGCTGCTTCTAGAATTCCG
GCTGATCATATGGTTTTAATGGCGGGTTTTACGGCTGGTAATGAAAAGGGGGAATTAGTG
GTTCTGGGTAGAAATGGGTCTGATTATAGCGCGGCTGTTTTAGCTGCTTGTTTACGGGCT
GATTGTTGTGAAATTTGGACGGATGTTGACGGTGTTTATACGTGTGACCCTAGACAAGTT
CCTGATGCTAGATTACTGAAGAGCATGAGCTATCAGGAGGCTATGGAATTAAGCTACTTC
GGGGCTAAAGTGTTACACCCGAGAACTATTACGCCTATTGCGCAATTTCAGATTCCGTGT
TTAATCAAGAACACGGGGAACCCGCAAGCTCCTGGTACTTTAATTGGGGCTTCTAGAGAT
GAAGATGAACTGCCTGTTAAAGGGATTAGCAATCTGAACAACATGGCGATGTTTAGCGTG
TCTGGGCCTGGTATGAAAGGTATGGTTGGTATGGCTGCTAGAGTTTTTGCTGCTATGTCT
AGAGCTAGAATTAGCGTTGTGTTAATCACGCAGTCTAGCTCTGAATACAGCATTAGCTTC
TGCGTGCCTCAATCTGATTGCGTTAGAGCGGAAAGAGCTATGCAAGAAGAATTTTACCTG
GAGCTGAAAGAGGGGTTACTGGAACCTTTAGCGGTTACTGAAAGACTGGCTATTATCAGC
GTTGTGGGTGATGGTATGAGAACTTTACGGGGTATTAGCGCTAAATTCTTCGCGGCTTTA
GCTAGAGCTAATATCAACATCGTGGCGATTGCGCAAGGTTCTTCTGAAAGATCTATCAGC
GTTGTGGTTAACAACGACGACGCTACTACTGGTGTTAGAGTTACTCACCAAATGCTGTTT
AACACGGACCAGGTTATTGAGGTGTTTGTGATCGGGGTTGGTGGTGTTGGTGGTGCTTTA
TTAGAACAACTGAAACGGCAACAATCTTGGTTAAAGAACAAGCACATCGACCTGCGGGTT
TGTGGTGTTGCTAATTCTAAGGCGTTACTGACTAATGTGCACGGTTTAAACCTGGAGAAT
TGGCAGGAAGAGTTAGCGCAAGCTAAAGAGCCTTTTAACCTGGGTAGATTAATCCGGTTA
GTGAAGGAGTACCACTTACTGAACCCGGTTATTGTGGACTGTACTAGCTCTCAAGCGGTT
GCTGATCAATATGCGGATTTTCTGAGAGAGGGTTTTCACGTTGTTACGCCTAATAAGAAG
GCGAATACGAGCTCTATGGACTATTACCACCAGTTACGGTATGCGGCTGAAAAAAGCAGA
AGAAAGTTCCTGTACGACACGAATGTGGGGGCTGGTTTACCTGTTATTGAAAATCTGCAG
AATCTGCTGAACGCGGGTGATGAATTAATGAAGTTCAGCGGGATTCTGTCTGGTTCTTTA
AGCTACATCTTCGGGAAACTGGACGAAGGGATGTCTTTTAGCGAAGCGACTACTTTAGCG
AGAGAAATGGGGTATACTGAGCCTGATCCTAGAGATGATTTAAGCGGGATGGATGTTGCT
AGAAAACTGCTGATTCTGGCGAGAGAAACTGGTAGAGAATTAGAGCTGGCTGATATTGAG
ATTGAGCCGGTTTTACCGGCTGAATTTAACGCGGAAGGTGATGTTGCTGCTTTTATGGCT
AATCTGTCTCAGTTAGACGACTTATTCGCGGCTAGAGTTGCTAAAGCGAGAGATGAAGGT
AAAGTGTTACGGTATGTGGGGAATATTGACGAGGATGGGGTTTGTAGAGTTAAAATCGCG
GAAGTGGATGGGAATGATCCGTTATTTAAGGTGAAGAACGGGGAAAACGCGTTAGCGTTT
TATAGCCACTACTACCAGCCGTTACCTTTAGTGTTACGGGGTTATGGGGCTGGTAATGAT
GTTACTGCTGCTGGTGTTTTTGCTGATTTACTGAGAACGTTAAGCTGGAAACTGGGGGTT
...

GCF_000005845.2_ASM584v2_protein.gc35.fna

>NP_414542.1 thr operon leader peptide [Escherichia coli str. K-12 substr. MG1655] | Resulting GC: 39.68%
ATGAAGCGGATTTCTACTACTATTACGACTACTATTACGATTACGACTGGTAATGGTGCT
GGT
>NP_414543.1 fused aspartate kinase/homoserine dehydrogenase 1 [Escherichia coli str. K-12 substr. MG1655] | Resulting GC: 35.08%
ATGCGGGTTTTAAAATTCGGGGGTACTTCTGTTGCTAATGCTGAAAGATTTTTAAGAGTT
GCTGATATTTTAGAGTCTAATGCGAGACAAGGTCAAGTTGCTACTGTTTTATCTGCTCCT
GCTAAAATTACTAATCATTTAGTTGCTATGATTGAAAAAACGATTAGCGGTCAAGATGCT
TTACCTAATATTAGCGATGCTGAAAGAATTTTTGCGGAATTATTAACGGGTTTAGCTGCT
GCTCAACCTGGTTTTCCTTTAGCTCAATTAAAAACTTTTGTTGATCAAGAATTTGCTCAA
ATTAAGCACGTTTTACACGGTATTTCTTTACTGGGTCAATGTCCTGATTCTATTAATGCT
GCTTTAATTTGCAGAGGTGAAAAAATGTCTATTGCGATTATGGCTGGTGTTTTAGAAGCT
AGAGGTCATAATGTTACTGTTATTGATCCTGTTGAAAAATTACTGGCTGTTGGTCATTAT
TTAGAGTCTACTGTTGATATTGCGGAATCTACTAGAAGAATTGCTGCTTCTAGAATTCCT
GCTGATCATATGGTTTTAATGGCTGGTTTTACTGCTGGTAATGAAAAAGGTGAATTAGTT
GTTTTAGGTAGAAATGGTTCTGATTATTCTGCTGCTGTTTTAGCTGCTTGTTTAAGAGCT
GATTGTTGTGAAATTTGGACTGATGTTGATGGTGTTTATACTTGTGATCCTAGACAAGTT
CCTGATGCTAGATTATTAAAATCTATGTCTTATCAAGAAGCTATGGAATTATCTTATTTC
GGGGCTAAAGTTTTACACCCTAGAACTATTACTCCTATTGCTCAATTTCAAATTCCGTGT
TTAATCAAGAACACGGGTAATCCTCAAGCTCCTGGTACTTTAATTGGTGCTTCTAGAGAT
GAAGATGAATTACCTGTTAAAGGTATTTCTAATTTAAATAACATGGCGATGTTTTCTGTT
TCTGGGCCTGGTATGAAAGGTATGGTTGGTATGGCTGCTAGAGTTTTTGCTGCTATGTCT
AGAGCTAGAATTTCTGTTGTTTTAATTACTCAATCTTCTTCTGAATATTCTATTTCTTTT
TGTGTTCCTCAATCTGATTGTGTTAGAGCTGAAAGAGCTATGCAAGAAGAATTTTATTTA
GAACTGAAAGAGGGTTTATTAGAGCCTTTAGCTGTTACTGAAAGATTAGCTATTATTAGC
GTTGTGGGTGATGGTATGAGAACTTTAAGAGGTATTTCTGCTAAATTTTTTGCGGCTTTA
GCTAGAGCTAATATTAATATCGTGGCTATTGCTCAAGGTTCTTCTGAAAGATCTATTTCT
GTTGTTGTTAATAACGACGATGCTACTACTGGTGTTAGAGTTACTCATCAAATGTTATTT
AATACGGACCAAGTTATTGAGGTTTTTGTGATTGGGGTTGGTGGTGTTGGTGGTGCTTTA
TTAGAACAATTAAAAAGACAACAATCTTGGTTAAAAAATAAGCACATTGACTTACGGGTT
TGTGGTGTTGCTAATTCTAAAGCTTTATTAACGAATGTGCATGGTTTAAATCTGGAAAAT
TGGCAGGAAGAATTAGCGCAAGCTAAAGAACCTTTTAATTTAGGGAGATTAATTCGGTTA
GTTAAGGAGTATCACTTACTGAATCCGGTTATTGTTGATTGTACTTCTTCTCAAGCTGTT
GCTGATCAATATGCTGATTTTTTACGGGAAGGTTTTCATGTTGTTACTCCTAATAAAAAA
GCGAATACGTCTTCTATGGATTATTACCACCAATTACGGTATGCTGCTGAAAAATCTAGA
AGAAAATTCCTGTATGACACTAATGTGGGTGCTGGTTTACCTGTTATTGAAAATTTACAA
AATCTGCTGAATGCGGGTGATGAATTAATGAAATTTAGCGGTATTTTAAGCGGTTCTTTA
TCTTACATCTTCGGGAAATTAGACGAAGGTATGTCTTTTTCTGAAGCTACTACTTTAGCT
AGAGAAATGGGTTATACTGAACCTGATCCTAGAGATGATTTATCTGGTATGGATGTTGCT
AGAAAATTATTAATCCTGGCTAGAGAAACTGGTAGAGAATTAGAATTAGCTGATATTGAA
ATTGAGCCGGTTTTACCTGCTGAATTTAATGCTGAAGGTGATGTTGCTGCTTTTATGGCT
AATTTATCTCAATTAGATGATTTATTCGCGGCTAGAGTTGCTAAAGCTAGAGATGAAGGT
AAAGTTTTAAGATATGTTGGTAATATTGACGAAGATGGTGTTTGTAGAGTTAAAATTGCG
GAAGTTGATGGTAATGATCCTTTATTTAAGGTGAAAAACGGGGAAAATGCTTTAGCTTTT
TATAGCCACTATTACCAGCCTTTACCTTTAGTTTTACGGGGTTATGGTGCTGGTAATGAT
GTTACTGCTGCTGGTGTTTTTGCTGATTTATTAAGAACTTTATCTTGGAAATTAGGTGTT
...

GCF_000005845.2_ASM584v2_protein.gc35_report.tsv

id      length  theoretical_min_gc      theoretical_max_gc      actual_gc       note
NP_414542.1     63      30.158730158730158      63.49206349206349       39.682539682539684
NP_414543.1     2460    30.48780487804878       68.21138211382114       35.081300813008134
NP_414544.1     930     33.01075268817204       70.0    35.16129032258065
NP_414545.1     1284    29.906542056074763      67.91277258566979       35.046728971962615
NP_414546.1     294     37.07482993197279       72.10884353741497       40.476190476190474      desired GC% unreachable; adjusted to theoretical min
NP_414547.1     774     25.839793281653744      64.08268733850129       35.012919896640824
NP_414548.1     1428    31.72268907563025       67.78711484593838       35.22408963585434
NP_414549.1     951     29.02208201892745       66.5615141955836        34.910620399579386
NP_414550.1     585     32.30769230769231       70.25641025641025       35.72649572649573
...

GCF_000005845.2_ASM584v2_protein.gc45_report.tsv

id      length  theoretical_min_gc      theoretical_max_gc      actual_gc       note
NP_414542.1     63      30.158730158730158      63.49206349206349       49.2063492063492
NP_414543.1     2460    30.48780487804878       68.21138211382114       45.040650406504064
NP_414544.1     930     33.01075268817204       70.0    44.946236559139784
NP_414545.1     1284    29.906542056074763      67.91277258566979       45.01557632398754
NP_414546.1     294     37.07482993197279       72.10884353741497       45.23809523809524
NP_414547.1     774     25.839793281653744      64.08268733850129       44.96124031007752
NP_414548.1     1428    31.72268907563025       67.78711484593838       45.02801120448179
NP_414549.1     951     29.02208201892745       66.5615141955836        44.900105152471085
NP_414550.1     585     32.30769230769231       70.25641025641025       44.95726495726496
...

GCF_000005845.2_ASM584v2_protein.gc55_report.tsv

id      length  theoretical_min_gc      theoretical_max_gc      actual_gc       note
NP_414542.1     63      30.158730158730158      63.49206349206349       57.14285714285714
NP_414543.1     2460    30.48780487804878       68.21138211382114       55.00000000000001
NP_414544.1     930     33.01075268817204       70.0    54.83870967741935
NP_414545.1     1284    29.906542056074763      67.91277258566979       54.82866043613706
NP_414546.1     294     37.07482993197279       72.10884353741497       55.44217687074829
NP_414547.1     774     25.839793281653744      64.08268733850129       55.03875968992248
NP_414548.1     1428    31.72268907563025       67.78711484593838       54.971988795518214
NP_414549.1     951     29.02208201892745       66.5615141955836        54.99474237644585
NP_414550.1     585     32.30769230769231       70.25641025641025       55.042735042735046
...