'I can't donwload complete genome of Culex pipiens pallens of the ncbi by API (Entrez): HTTP Error 400: Bad Request
I am trying to download the genbank if possible of the complete genome of Culex pipiens pallens from the ncbi but I get this error. The URL of de ncbi. In the db variable that I sent in the fetch I already tried with nucleotide, genome, Gen etc. I thought that with assembly I would download it but no.
When I run the download_genbank() function, I get the error: HTTP Error 400: Bad Request
This is the page:
ncbi culex pipiens pallens complete genome:
from pathlib import Path
from Bio import Entrez
from Bio.Entrez.Parser import DictionaryElement, ListElement
from Bio import SeqIO
from Bio.SeqRecord import SeqRecord
from typing import Union
def write_text(txt: str, filename: str):
Path(filename).parent.mkdir(parents=True, exist_ok=True)
Path(filename).write_text(txt)
def request_fetch( db:str,
id: Union[str, list[str], set[str]],
file_format: str,
filename: str ):
""" This function writes plain text in the type you specify.
Typical types: 'fasta', 'gb', etc.
Should be used to download only a few files."""
if Path(filename).exists(): return
with Entrez.efetch( db=db,
id=id,
rettype=file_format,
retmode="text" ) as response:
content: str = response.read()
write_text(content, filename)
#GCF_016801865.1
def downloand_genbank():
request_fetch( db="assembly",
id='GCF_016801865.1',
file_format='gb',
filename='cache/culex_pipens_pallens.gb')
download_genbank()
Sources
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Source: Stack Overflow
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