Getting protein sequences by accessing Uniprot (with Python)

Question

I have a list of protein id's I'm trying to access the protein sequences from Uniprot with python. I came across this post :Protein sequence from uniprot protein id python but gives a list of elements and not the actual sequence:

Code

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'))

which gives output:

output

[SeqRecord(seq=Seq('MQAALIGLNFPLQRRFLSGVLTTTSSAKRCYSGDTGKPYDCTSAEHKKELEECY...SSS', SingleLetterAlphabet()), id='sp|O45228|PROD_CAEEL', name='sp|O45228|PROD_CAEEL', description='sp|O45228|PROD_CAEEL Proline dehydrogenase 1, mitochondrial OS=Caenorhabditis elegans OX=6239 GN=prdh-1 PE=2 SV=2', dbxrefs=[])]

I was just curious on how I can actually get the sequence itself.

Pallie · Accepted Answer · 2020-09-21T13:18:32.687

3

[record.seq for record in pSeq]

edit: You'll want str(pSeq[0].seq)

edited Sep 21 '20 at 13:18

answered Sep 21 '20 at 13:06

Pallie

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This only gives partial sequence, stores the elements as a list. – bioinformatics_student Sep 21 '20 at 13:13
1

@bioinformatics_student, check the elements in your list again – StupidWolf Sep 21 '20 at 13:19
I get a lot of elements out of range for certain proteins, probably because some elements are returned as empty items. – bioinformatics_student Sep 21 '20 at 15:43
1

you can wrap it with error handling (https://docs.python.org/3/tutorial/errors.html#handling-exceptions) or write an `if len(pSeq) > 1:` that checks if the query returned empty or not – Pallie Sep 22 '20 at 06:58

Getting protein sequences by accessing Uniprot (with Python)

Code

output

1 Answers1