Protein sequence from uniprot protein id python

Question

I was wondering if there is way to get the sequence of proteins from uniprot protein ids. I did check few online softwares but they allow to get one sequence at a time but I have 5536 vlues. Is there any package in biopython to do this?

Answer 1

All the sequences from uniprot can be accesed from "http://www.uniprot.org/uniprot/" + UniprotID +.fasta. You can obtain any sequence with

import requests as r
from Bio import SeqIO
from io import StringIO

cID='P04637'

baseUrl="http://www.uniprot.org/uniprot/"
currentUrl=baseUrl+cID+".fasta"
response = r.post(currentUrl)
cData=''.join(response.text)

Seq=StringIO(cData)
pSeq=list(SeqIO.parse(Seq,'fasta'))

cID can be a list or a single entry, if you loop trough a bug list just add a delay between downloads, trying not to saturate the server. Hope it helps