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"""
Copyright 2020 Kat Holt
Copyright 2020 Ryan Wick (rrwick@gmail.com)
https://github.com/katholt/Kleborate/
This file is part of Kleborate. Kleborate is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by the Free Software Foundation,
either version 3 of the License, or (at your option) any later version. Kleborate is distributed in
the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
details. You should have received a copy of the GNU General Public License along with Kleborate. If
not, see <http://www.gnu.org/licenses/>.
"""
import unittest
from kleborate.contig_stats import get_contig_stats, get_qc_warnings
class TestContigStats(unittest.TestCase):
def test_count_1(self):
contig_count, _, _, _, _ = get_contig_stats('test/test_contig_stats/contig_stats_1.fasta')
self.assertEqual(contig_count, 4)
def test_count_2(self):
contig_count, _, _, _, _ = get_contig_stats('test/test_contig_stats/contig_stats_2.fasta')
self.assertEqual(contig_count, 3)
def test_n50_1(self):
_, n50, _, _, _ = get_contig_stats('test/test_contig_stats/contig_stats_1.fasta')
self.assertEqual(n50, 40)
def test_n50_2(self):
_, n50, _, _, _ = get_contig_stats('test/test_contig_stats/contig_stats_2.fasta')
self.assertEqual(n50, 200)
def test_longest_1(self):
_, _, longest_contig, _, _ = get_contig_stats('test/test_contig_stats/contig_stats_1.fasta')
self.assertEqual(longest_contig, 45)
def test_longest_2(self):
_, _, longest_contig, _, _ = get_contig_stats('test/test_contig_stats/contig_stats_2.fasta')
self.assertEqual(longest_contig, 200)
def test_ambiguous_bases_1(self):
_, _, _, _, ambiguous = get_contig_stats('test/test_contig_stats/contig_stats_1.fasta')
self.assertEqual(ambiguous, 'no')
def test_ambiguous_bases_2(self):
_, _, _, _, ambiguous = get_contig_stats('test/test_contig_stats/contig_stats_2.fasta')
self.assertEqual(ambiguous, 'yes (1)')
def test_ambiguous_bases_3(self):
_, _, _, _, ambiguous = get_contig_stats('test/test_contig_stats/contig_stats_3.fasta')
self.assertEqual(ambiguous, 'no')
def test_ambiguous_bases_4(self):
_, _, _, _, ambiguous = get_contig_stats('test/test_contig_stats/contig_stats_4.fasta')
self.assertEqual(ambiguous, 'yes (4)')
def test_total_size_1(self):
_, _, _, total_size, _ = get_contig_stats('test/test_contig_stats/contig_stats_1.fasta')
self.assertEqual(total_size, 115)
def test_total_size_2(self):
_, _, _, total_size, _ = get_contig_stats('test/test_contig_stats/contig_stats_2.fasta')
self.assertEqual(total_size, 260)
def test_total_size_3(self):
_, _, _, total_size, _ = get_contig_stats('test/test_contig_stats/contig_stats_3.fasta')
self.assertEqual(total_size, 260)
def test_total_size_4(self):
_, _, _, total_size, _ = get_contig_stats('test/test_contig_stats/contig_stats_4.fasta')
self.assertEqual(total_size, 260)
def test_qc_warnings_1(self):
# A perfectly nice assembly - yields no warnings.
warnings = get_qc_warnings(5500000, 250000, 'no', True)
self.assertEqual(warnings, '-')
def test_qc_warnings_2(self):
# Large assembly size.
warnings = get_qc_warnings(10000000, 250000, 'no', True)
self.assertEqual(warnings, 'total_size')
def test_qc_warnings_3(self):
# Large assembly size, but not KpSC so no warning.
warnings = get_qc_warnings(10000000, 250000, 'no', False)
self.assertEqual(warnings, '-')
def test_qc_warnings_4(self):
# Small assembly size.
warnings = get_qc_warnings(2000000, 250000, 'no', True)
self.assertEqual(warnings, 'total_size')
def test_qc_warnings_5(self):
# Small assembly size, but not KpSC so no warning.
warnings = get_qc_warnings(2000000, 250000, 'no', False)
self.assertEqual(warnings, '-')
def test_qc_warnings_6(self):
# Small N50.
warnings = get_qc_warnings(5500000, 1000, 'no', True)
self.assertEqual(warnings, 'N50')
def test_qc_warnings_7(self):
# Has ambiguous bases
warnings = get_qc_warnings(5500000, 250000, 'yes (50)', True)
self.assertEqual(warnings, 'ambiguous_bases')
def test_qc_warnings_8(self):
# All three warnings.
warnings = get_qc_warnings(2000000, 1000, 'yes (1000)', True)
self.assertEqual(warnings, 'total_size,N50,ambiguous_bases')
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