1
$\begingroup$

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'].

$\endgroup$
1
$\begingroup$

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')

$\endgroup$
3

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.