retrieve_gene.py

gistfile1.py

from Bio import Entrez

def fetch_gene_coordinates(search_term):
    handle = Entrez.esearch(db="gene", term=search_term)
    rec = Entrez.read(handle)
    gene_id = rec["IdList"][0] # assuming best match works
    
    handle = Entrez.efetch(db="gene", id=gene_id, retmode="xml")
    rec = Entrez.read(handle)[0]
    gene_locus = rec["Entrezgene_locus"][0]
    region = gene_locus["Gene-commentary_seqs"][0]["Seq-loc_int"]["Seq-interval"]
    start = int(region["Seq-interval_from"]) + 1
    end = int(region["Seq-interval_to"]) + 1 
    gi_id = region["Seq-interval_id"]["Seq-id"]["Seq-id_gi"]
    strand = region["Seq-interval_strand"]["Na-strand"].attributes["value"]
    return gi_id, start, end, strand
    
def get_fasta_seq(gi_id, start, end, strand):
    strand = 2 if strand.lower() == "minus" else 1
    handle = Entrez.efetch(db="nucleotide", rettype="fasta", id=gi_id,
            seq_start=start, seq_stop=end, strand=strand)
    return handle.read()
    
Entrez.email = "yours@mail.com"
search_term = "fliC ct18"

gi_id, start, end, strand = fetch_gene_coordinates(search_term)
print get_fasta_seq(gi_id, start, end, strand)