Entering edit mode
3.5 years ago
charlieclark1ee
▴
20
I have the following Python code in which I am trying to get the sequence of a TMV replicase gene:
# Lookup ID
search = Entrez.esearch(db='gene', term='Tobacco mosaic virus[Orgn] replicase', idtype="acc")
read = Entrez.read(search)
idlist = read["IdList"]
# Get sequence
search = Entrez.efetch(db='gene', id=idlist[0], retmode='text', rettype='gb')
read = SeqIO.read(search, "genbank")
sequence = read.seq
However, using idtype="acc"
doesn't give me an accession number. Instead, I get 1494081, the ID for the gene in the gene
database.
When I then try and fetch it in the gene database it throws ValueError: No records found in handle
.
I've also tried fetching with the nucleotide database but without the accession number the ID leads to the wrong thing.
Using EntrezDirect:
To get the sequence
Is there an equivalent to
xtract
for biopython? I can't seem to find one.