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# Copyright 2019 by Sergio Valqui. All rights reserved.
# This file is part of the Biopython distribution and governed by your
# choice of the "Biopython License Agreement" or the "BSD 3-Clause License".
# Please see the LICENSE file that should have been included as part of this
# package.
"""Unit tests for the Bio.UniProt.GOA Module.
GOA files can be found here ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/
"""
import unittest
import tempfile
import os
from Bio.UniProt import GOA
class GoaTests(unittest.TestCase):
"""Test for UniProt GOA Files."""
def test_gaf_iterator(self):
"""Test GOA GAF file iterator."""
# Test GAF 2.0
recs = []
with open("UniProt/goa_yeast.gaf") as handle:
for rec in GOA.gafiterator(handle):
recs.append(rec)
# Check number of records
self.assertEqual(len(recs), 587)
# Check keys are same as predefined fields
self.assertEqual(sorted(recs[0].keys()), sorted(GOA.GAF20FIELDS))
# Check values of first record
self.assertEqual(recs[0]["DB"], "UniProtKB")
self.assertEqual(recs[0]["DB_Object_ID"], "A0A023PXA5")
self.assertEqual(recs[0]["DB_Object_Symbol"], "YAL019W-A")
self.assertEqual(recs[0]["Qualifier"], [""])
self.assertEqual(recs[0]["GO_ID"], "GO:0003674")
self.assertEqual(recs[0]["DB:Reference"], ["GO_REF:0000015"])
self.assertEqual(recs[0]["Evidence"], "ND")
self.assertEqual(recs[0]["With"], [""])
# Test GAF 2.1, it has the same fields as GAF 2.0
recs = []
with open("UniProt/gene_association.goa_yeast.1.gaf") as handle:
for rec in GOA.gafiterator(handle):
recs.append(rec)
# Check number of records
self.assertEqual(len(recs), 300)
# Check keys are same as predefined fields
self.assertEqual(sorted(recs[0].keys()), sorted(GOA.GAF20FIELDS))
# Check values of first record
self.assertEqual(recs[0]["DB"], "UniProtKB")
self.assertEqual(recs[0]["DB_Object_ID"], "P17536")
self.assertEqual(recs[0]["DB_Object_Symbol"], "TPM1")
self.assertEqual(recs[0]["Qualifier"], [""])
self.assertEqual(recs[0]["GO_ID"], "GO:0000001")
self.assertEqual(recs[0]["DB:Reference"], ["PMID:10652251"])
self.assertEqual(recs[0]["Evidence"], "TAS")
self.assertEqual(recs[0]["With"], [""])
def test_gpa_iterator(self):
"""Test GOA GPA file iterator."""
recs = []
with open("UniProt/goa_yeast.gpa.59.gpa") as handle:
for rec in GOA.gpa_iterator(handle):
recs.append(rec)
self.assertEqual(len(recs), 300)
self.assertEqual(sorted(recs[0].keys()), sorted(GOA.GPA11FIELDS))
# Check values of first record
self.assertEqual(recs[0]["DB"], "UniProtKB")
self.assertEqual(recs[0]["DB_Object_ID"], "A0A023PXA5")
self.assertEqual(recs[0]["Qualifier"], ["enables"])
self.assertEqual(recs[0]["GO_ID"], "GO:0003674")
self.assertEqual(recs[0]["DB:Reference"], ["GO_REF:0000015"])
self.assertEqual(recs[0]["ECO_Evidence_code"], "ECO:0000307")
self.assertEqual(recs[0]["With"], [""])
self.assertEqual(recs[0]["Interacting_taxon_ID"], "")
self.assertEqual(recs[0]["Date"], "20030730")
self.assertEqual(recs[0]["Assigned_by"], "SGD")
self.assertEqual(recs[0]["Annotation Extension"], [""])
self.assertEqual(recs[0]["Annotation_Properties"], "go_evidence=ND")
def test_gpi_iterator(self):
"""Test GOA GPI file iterator."""
recs = []
with open("UniProt/gp_information.goa_yeast.28.gpi") as handle:
for rec in GOA.gpi_iterator(handle):
recs.append(rec)
self.assertEqual(len(recs), 300)
self.assertEqual(sorted(recs[0].keys()), sorted(GOA.GPI11FIELDS))
# Check values of first record
self.assertEqual(recs[0]["DB_Object_ID"], "A2P2R3")
self.assertEqual(recs[0]["DB_Object_Symbol"], "YMR084W")
self.assertEqual(
recs[0]["DB_Object_Name"],
[
"Putative glutamine--fructose"
"-6-phosphate aminotransferase"
" [isomerizing]"
],
)
self.assertEqual(recs[0]["DB_Object_Synonym"], ["YM084_YEAST", "YMR084W"])
self.assertEqual(recs[0]["DB_Object_Type"], "protein")
self.assertEqual(recs[0]["Taxon"], "taxon:559292")
self.assertEqual(recs[0]["Parent_Object_ID"], "")
self.assertEqual(recs[0]["DB_Xref"], [""])
self.assertEqual(recs[0]["Gene_Product_Properties"], ["db_subset=Swiss-Prot"])
def test_selection_writing(self):
"""Test record_has, and writerec.
Adapted from Bio.UniProt.GOA.py by Iddo Friedberg idoerg@gmail.com.
"""
recs = []
filtered = []
# Fields to filter
evidence = {"Evidence": {"ND"}}
synonym = {"Synonym": {"YA19A_YEAST", "YAL019W-A"}}
taxon_id = {"Taxon_ID": {"taxon:559292"}}
# Temporal file to test writerec
f_number, f_filtered = tempfile.mkstemp()
os.close(f_number)
# Open a file and select records as per filter
with open("UniProt/goa_yeast.gaf") as handle:
for rec in GOA.gafiterator(handle):
recs.append(rec)
# Filtering
if (
GOA.record_has(rec, taxon_id)
and GOA.record_has(rec, evidence)
and GOA.record_has(rec, synonym)
):
filtered.append(rec)
# Check number of filtered records
self.assertEqual(len(filtered), 3)
# Write the filtered records to a file using writerec
with open(f_filtered, "w") as handle:
# '!gaf-version: 2.1'
handle.write("!gaf-version: 2.1 \n") # Adding file header
for rec in filtered:
GOA.writerec(rec, handle)
# Open and read the file containing the filtered records
recs_ff = [] # Records from filtered file
with open(f_filtered) as handle:
for rec in GOA.gafiterator(handle):
recs_ff.append(rec)
# Delete test file
os.remove(f_filtered)
# Compare, recs saved by writerec and filtered recs
self.assertEqual(filtered, recs_ff)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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