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I'm trying to use Entrez (through Biopython) to download the sequence of a TMV replicase gene.

I have the following code:

# Lookup ID
search = Entrez.esearch(db='gene', term='Tobacco mosaic virus[Orgn] AND replicase')
read = Entrez.read(search)
idlist = read["IdList"]

# Fetch sequence
search = Entrez.efetch(db='gene', id=idlist[0], retmode='text', rettype='gb')
read = SeqIO.read(search, "genbank")
tmv_replicase = read.seq

But when I run it it throws the exception on the SeqIO.read line: ValueError: No records found in handle.

The IDs provided in idlist are: ['1494081', '1494082'].

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1 Answer 1

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Did you try to fetch from the database nucleotide instead of gene ?

# load modules
from Bio import SeqIO
from Bio import Entrez

# Lookup ID
search = Entrez.esearch(db='nucleotide', term='Tobacco mosaic virus[Orgn] AND replicase')
read = Entrez.read(search)
idlist = read["IdList"]

# Fetch sequence
search = Entrez.efetch(db='nucleotide', id=idlist[0], retmode='text', rettype='gb')
read = SeqIO.read(search, "genbank")
tmv_replicase = read.seq

It returns

>>> read
SeqRecord(seq=Seq('GTATTTTTACAACAATTACCAACAACAACAAACAACAAACAACATTACAATTAC...GGG'), id='MN912489.1', name='MN912489', description='Tobacco mosaic virus isolate TMV:BR:SC:02:01, complete genome', dbxrefs=[])
>>> tmv_replicase
Seq('GTATTTTTACAACAATTACCAACAACAACAAACAACAAACAACATTACAATTAC...GGG')
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  • $\begingroup$ Thank you, this gets me what I wanted. Out of interest though, do you know why using the gene database for this wouldn't work? (I'm new to Entrez). $\endgroup$
    – blammo69
    Commented Jun 3, 2021 at 9:34
  • $\begingroup$ It is simply 2 differents databases. The ID into nucleotide is not the same into gene. Thus from the website NCBI it is possible to extract a fasta from a gene query it doesn't seem possible with biopython biopython.readthedocs.io/en/latest/chapter_entrez.html $\endgroup$
    – Pierre-Edouard Guerin
    Commented Jun 4, 2021 at 8:03
  • $\begingroup$ If you want to filter your queries from the nucleotide database in order to get only the specific genes you can check my code as an example: gitlab.mbb.univ-montp2.fr/bev/target_genes_from_ncbi/-/blob/… $\endgroup$
    – Pierre-Edouard Guerin
    Commented Jun 4, 2021 at 8:05

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