def ncbi_efetch(name, gbk_name, db=None):
"""
Connects to Entrez Direct to download data.
"""
# Get the entire GenBank file.
format, retmode = "gbwithparts", "text"
# Guess accession numbers that are proteins.
if name[:2] in ["AP", "NP", "YP", "XP", "WP", "AK"]:
db = db or "protein"
else:
db = db or "nuccore"
try:
logger.info(f"connecting to Entrez for {name}")
stream = Entrez.efetch(id=name, db=db, rettype=format, retmode=retmode)
except Exception as exc:
msg = f"{exc} for efetch acc={name} db={db} format={format} mode={retmode}"
utils.error(msg)
# Save the stream to GenBank.
utils.save_stream(stream=stream, fname=gbk_name)
def genbank_save(name, fname, db=None):
"""
Connects to Entrez Direct to download data.
"""
# Get the entire GenBank file.
format, retmode = "gbwithparts", "text"
# Guess accession numbers that are proteins.
# https: // www.ncbi.nlm.nih.gov / Sequin / acc.html
if utils.maybe_prot(name):
db = db or "protein"
else:
db = db or "nuccore"
try:
logger.info(f"connecting to Entrez for {name}")
stream = Entrez.efetch(id=name, db=db, rettype=format, retmode=retmode)
except Exception as exc:
msg = f"{exc} for efetch acc={name} db={db} format={format} mode={retmode}"
utils.error(msg)
# Save the stream to GenBank.
utils.save_stream(stream=stream, fname=fname)