dataset_script.py

import wget
import re
from Bio import SeqIO
import pandas as pd

def load_fasta_into_list(fasta_file):
    """
    Load the FASTA file into a dictionary for quick lookup.

    :param fasta_file: Path to the FASTA file
    :return: List of dictionaries with processed sequences as keys and (id, description) as values
    """
    fasta_list = []
    scop_pattern = re.compile(r'\b[a-z]\.\d+\.\d+\.\d+\b')

    for record in SeqIO.parse(fasta_file, "fasta"):
        processed_sequence = str(record.seq)
        fasta_list.append({
            "id": record.id,
            "primary" : processed_sequence,
            "class": ".".join(record.description.split(" ")[1].split(".")[:-3]),
            "fold": ".".join(record.description.split(" ")[1].split(".")[:-2]),
            "super_family": ".".join(record.description.split(" ")[1].split(".")[:-1]),
            "family": record.description.split(" ")[1],
            "description": record.description,
        })
    return fasta_list

def should_exclude(record):
    deets = record.description.split(" ")[1]
    # print(deets)
    fold = ".".join(deets.split(".")[:2])
    return fold in excluded_folds

# URL of the file to download
url = "https://scop.berkeley.edu/downloads/scopeseq-2.08/astral-scopedom-seqres-gd-sel-gs-bib-40-2.08.fa"

# Download the file
file_name = wget.download(url)
print(f"\nDownloaded file: {file_name}")


excluded_folds = ['c.2', 'c.3', 'c.4', 'c.5', 'c.27', 'c.28', 'c.30', 'c.31', 'b.66', 'b.67', 'b.68', 'b.69', 'b.70']

fasta_list = [item for item in load_fasta_into_list(file_name) if item['fold'] not in excluded_folds]

df = pd.DataFrame(fasta_list)

df.to_csv('full_data.csv', index=False)

print(len(df))