get_odb.py

#!/usr/bin/env python3

import argparse
import os
import json
import sys
import requests
import re


def parse_args(args=None):
    Description = "Get ODB database value using GOAT API"

    parser = argparse.ArgumentParser(description=Description)
    parser.add_argument("ASSEMBLY", help="Assembly GCA value.")
    parser.add_argument("FILE_OUT", help="Output CSV file.")
    parser.add_argument("--version", action="version", version="%(prog)s 1.0")
    return parser.parse_args(args)


def make_dir(path):
    if len(path) > 0:
        os.makedirs(path, exist_ok=True)


def get_odb(asm, file_out):
    # Using API, get JSON file with all associated ODB10 databases
    response = requests.get(
        "https://goat.genomehubs.org/api/v2/search?query=tax_lineage%28queryA.taxon_id%29&queryA=assembly--assembly_id%3D"
        + asm
        + "&result=taxon&fields=odb10_lineage"
    ).json()["results"]
    # Extract ODB10 lineage values
    odb_arr = [r["result"]["fields"]["odb10_lineage"]["value"] for r in response]
    # The closest [0] OBD10 lineage is selected, unless one of the lineage values is "eutheria", then choose "eutheria"
    odb_val = "eutheria_odb10" if "eutheria_odb10" in odb_arr else odb_arr[0]

    out_dir = os.path.dirname(file_out)
    make_dir(out_dir)

    with open(file_out, "w") as fout:
        print("busco_lineage", odb_val, sep=",", file=fout)


def main(args=None):
    args = parse_args(args)
    get_odb(args.ASSEMBLY, args.FILE_OUT)


if __name__ == "__main__":
    sys.exit(main())