Retrieve NCBI assembly accessions from GenBank accessions using E-utilities

retrieve_assembly_accession.py

import subprocess

def get_assembly_accession(genbank_accession):
    p1 = subprocess.Popen(
        ["elink", "-db", "nuccore", "-target", "assembly", "-id", genbank_accession],
        stdout=subprocess.PIPE,
        stderr=subprocess.PIPE,
    )
    p2 = subprocess.Popen(
        ["efetch", "-format", "docsum"],
        stdin=p1.stdout,
        stdout=subprocess.PIPE,
        stderr=subprocess.PIPE,
    )
    p3 = subprocess.Popen(
        ["xtract", "-pattern", "DocumentSummary", "-element", "AssemblyAccession"],
        stdin=p2.stdout,
        stdout=subprocess.PIPE,
        stderr=subprocess.PIPE,
        text=True,
    )
    stdout, stderr = p3.communicate()
    if p3.returncode:
        raise RuntimeError(stderr)
    return stdout.strip("\n")

get_assembly_accession("CP080583.1")