How to use EPOST and than use ESEARCH in biopython?

Question

I have a lit of gene ids:

id_list = ["19304878", "18606172", "16403221", "16377612", "14871861", "14630660"]

how I can take just the nucleotide sequence of this genes using EPOST and ESEARCH in biopython?

Answer 1

You probably want to be using efetch:

from Bio import SeqIO, Entrez

id_list = ["19304878", "18606172", "16403221", 
           "16377612", "14871861", "14630660"]

# Always tell NCBI who you are!
Entrez.email = "[email protected]"

# Fetch results from NCBI and write to output
with open("output.fa", "w") as out_handle:
    for gene_id in id_list:
        fa = Entrez.efetch(db="nucleotide", id=gene_id, rettype="fasta")
        SeqIO.write(SeqIO.parse(fa, "fasta"), out_handle, "fasta")

---

This is a python script that will do it:

get_fasta.py

$ python3 get_fasta.py -h
usage: get_fasta.py [-h] -e EMAIL -g GENES [-o OUTPUT]

Retrieve FASTA from NCBI using gene IDs

General options:
  -h, --help            Show this help and exit

Inputs:
  -e EMAIL, --email EMAIL
                        Your email address
  -g GENES, --genes GENES
                        A file containing a list of gene IDs, with one ID on
                        each line

Outputs:
  -o OUTPUT, --output OUTPUT
                        The file to write FASTA to. If not provided use STDOUT

---

#! /usr/bin/env python3

from argparse import ArgumentParser
from pathlib import Path
import sys

from Bio import SeqIO, Entrez


def main():
    # Get our command-line arguments
    parser, args = get_args()

    # Always tell NCBI who you are!
    Entrez.email = args.email

    # Check the input file is a file
    if not Path(args.genes).is_file():
        parser.error("--genes parameter must be a file")

    # Read in the gene IDs
    with open(args.genes, "r") as file_handle:
        id_list = [line.strip() for line in file_handle]

    #  Specify output as a file of STDOUT
    if args.output:
        out_handle = open(args.output, "w")
    else:
        out_handle = sys.stdout

    # Fetch results from NCBI and write to output
    for gene_id in id_list:
        fa = Entrez.efetch(db="nucleotide", id=gene_id, rettype="fasta")
        SeqIO.write(SeqIO.parse(fa, "fasta"), out_handle, "fasta")

    # Close handle if it's a file
    if out_handle is not sys.stdout:
        out_handle.close()


def get_args():
    parser = ArgumentParser(
        description="Retrieve FASTA from NCBI using gene IDs",
        add_help=False,
    )
    general = parser.add_argument_group(
        title='General options'
    )
    general.add_argument(
        "-h",
        "--help",
        action="help",
        help="Show this help and exit",
    )
    in_args = parser.add_argument_group(title='Inputs')
    in_args.add_argument(
        "-e",
        "--email",
        help="Your email address",
        required=True,
    )
    in_args.add_argument(
        "-g",
        "--genes",
        help="A file containing a list of gene IDs, with one ID on each line",
        required=True,
    )
    out_args = parser.add_argument_group(title='Outputs')
    out_args.add_argument(
        "-o",
        "--output",
        help="The file to write FASTA to. If not provided use STDOUT",
    )
    return parser, parser.parse_args()


if __name__ == "__main__":
    main()