Question: How to get all transcript and CDS from gene_id in biopython?
1
gravatar for ishenweiyan
10 weeks ago by
ishenweiyan10
ishenweiyan10 wrote:

I got the gene name and species, how can I retrieve all its transcript and CDS by the gene_id in python?

For example I get the gene symbol of TP53 (Gene ID: 7157),and I want to retrieve all its transcript and CDS sequences. How could I do it? Thank you very much.

from Bio import Entrez
Entrez.email = 'A.N.Other@example.com'
handle = Entrez.efetch(db="nucleotide", id=Accession_number, rettype="fasta", retmode="text")
record = handle.read()
biopython gene • 163 views
ADD COMMENTlink modified 10 weeks ago • written 10 weeks ago by ishenweiyan10

Could you develop what you want please

Is this what you are looking for ?

ADD REPLYlink written 10 weeks ago by Bastien Hervé3.3k

"asscess" == "Accession" ?

ADD REPLYlink written 10 weeks ago by jrj.healey10k

Yes, it should be Accession Number. Thanks for your kindly reminder.

ADD REPLYlink written 10 weeks ago by ishenweiyan10

You can take a look here

ADD REPLYlink written 10 weeks ago by Bastien Hervé3.3k
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