Downloading WGS contigs is easy with Biopython and Entrez if using the older sequence headers, such as:
> gi|351789644|gb|AEHK01402178.1|
This is done with:
from Bio import SeqIO
from Bio import Seq
from Bio import Entrez
Entrez.email = "[email protected]"
handle = Entrez.efetch(db="nucleotide", id=cntg, rettype="fasta", retmode="text")
record = SeqIO.read(handle, "fasta")
However, as of this year (2016), the new headers only have genebank numbers:
> gb|JSUE03030586.1|
Using the above 'nucleotide' database for Entrez does not produce a valid handle (i.e., the entrez query does not produce a record). I have tried different databases (e.g., "genome", "gene", "assembly", etc.) howerver, none of these produce valid queries.
Does anybody know of a solution?
From september 2016 there are removing gi from the records. May be that's causing problem in fetching.
I've found a way, not with entirely biopython. Will that work for you?
HI Ruhshan,
Indeed, this is part of the problem; the records are changing and the Entrez query has not caught up with the change. If you have a non-Biopython method, that would work for me.
Thanks.
D.
Hello David,
Please have a look at this code. Let me know if you have any difficulties understanding or running it.
Hi Ruhshan,
Thanks for your solution! I can make a small change to my code and bypasses the Entrez database issue; downloading directly from the wgs traces.
Thanks again.
Cheers,
David.
- Badges
- Science topic
- Similar topics
- Biological Science
- Molecular Biology
- Biomolecules
- Nucleic Acids
- RNA