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#!/usr/env/bin python3
from spoa import poa
from unittest import TestCase, main
class Tests(TestCase):
def test_bindings(self):
""" simple poa to check bindings"""
consensus, msa = poa(['AACTTATA', 'AACTTATG', 'AACTATA'])
self.assertEqual(consensus, 'AACTTATA')
self.assertEqual(len(msa), 3)
def test_bindings_no_msa(self):
""" simple poa to check bindings with msa generation"""
consensus, msa = poa(['AACTTATA', 'AACTTATG', 'AACTATA'], genmsa=False)
self.assertEqual(consensus, 'AACTTATA')
self.assertEqual(len(msa), 0)
def test_bindings_min_coverage(self):
""" simple poa to check bindings with `min_coverage` param"""
consensus, msa = poa(['AACTTATA', 'AACTTATG', 'AACTATA'], min_coverage=3)
self.assertEqual(consensus, 'AACTAT')
self.assertEqual(len(msa), 3)
def test_bindings_min_coverage_None(self):
""" simple poa to check bindings with `min_coverage=None`"""
consensus, msa = poa(['AACTTATA', 'AACTTATG', 'AACTATA'], min_coverage=None)
self.assertEqual(consensus, 'AACTTATA')
self.assertEqual(len(msa), 3)
def test_bindings_min_coverage_wrong_type_string(self):
""" check that bindings with `min_coverage=str` throw error"""
self.assertRaises(
RuntimeError, poa, ["AACTTATA", "AACTTATG", "AACTATA"], min_coverage="x"
)
def test_bindings_min_coverage_wrong_type_float(self):
""" check that bindings with `min_coverage=float` throw error"""
self.assertRaises(
RuntimeError, poa, ["AACTTATA", "AACTTATG", "AACTATA"], min_coverage=1.5
)
if __name__ == '__main__':
main()
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