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Quick script to download Uniprot info for proteins from Pfam trees (Newick tree format)

March 1, 2020, 7:14 am
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from ete3 import Tree
import sys
import os
import urllib.request
 
t = Tree(sys.argv[1])
 
for l in t:
        id = l.name.split("/")[0]
        print(f"Accession: {id}")
        if os.path.exists(f"{id}.txt") == False:
                print("Downloading...")
                page = urllib.request.urlopen(f"https://www.uniprot.org/uniprot/{id}.txt")
 
                out_file = open(f"{id}.txt","wb")
                out_file.write(page.read())
                out_file.close()
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