How to parse a Uniprot Dat file to retrieve GO in python?

Question

I have tried BioPython SeqIO and other parsers but couldn't find any good tool to parse DAT files.

https://omics.pnl.gov/software/uniprot-dat-file-parser

I have tried this one but they don't provide any gene annotations

http://biopython.org/wiki/SeqIO

They mostly talk about taking inputs of FASTA and not DAT file.

from Bio import SeqIO
   for record in SeqIO.parse("Fasta/f002", "fasta"):
...     print("%s %i" % (record.id, len(record)))

Answer 1

Those look like what Biopython calls "swiss" format, the plain text format used at SwissProt prior to it being called UniProt. Try:

from Bio import SeqIO
   for record in SeqIO.parse("example.dat", "swiss"):
       print("%s %i" % (record.id, len(record)))

See also the table for formats at http://biopython.org/wiki/SeqIO

Answer 2

Dear Muhammad Zeeshan,

you can use the query functions of the python library pyuniprot to get sequence (or many thing else)

• PyPi
• Read the docs

install (with pip or git clone) and update. Find out which taxonomy identifier fits to your organisms. Example here (human, mouse, rat). Don't make a full update for all organisms (takes very long).

pyuniprot.update(taxids=[9606, 10090, 10116])

Use following python code for your problem:

Assuming 1433E_HUMAN and A4_HUMAN are the identifier of interest:

Python code:

import pyuniprot
query = pyuniprot.query() 
entries = query.entry(name=('1433E_HUMAN', 'A4_HUMAN'))  
seqs = [x.sequence.sequence for x in entries]