Add unit tests

test/test_initial_check.py

@@ -0,0 +1,79 @@
+"""
+This module contains some tests for Trycycler. To run them, execute `pytest` from the root
+Trycycler directory.
+
+Copyright 2020 Ryan Wick ([email protected])
+https://github.com/rrwick/Trycycler
+
+This file is part of Trycycler. Trycycler 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. Trycycler 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 Trycycler.
+If not, see <http://www.gnu.org/licenses/>.
+"""
+
+import pytest
+
+import trycycler.initial_check
+
+
+def test_get_length_thresholds_1():
+    min_threshold, max_threshold = trycycler.initial_check.get_length_thresholds(1.5)
+    assert min_threshold == pytest.approx(0.6666666666667)
+    assert max_threshold == pytest.approx(1.5)
+
+
+def test_get_length_thresholds_2():
+    min_threshold, max_threshold = trycycler.initial_check.get_length_thresholds(2.0)
+    assert min_threshold == pytest.approx(0.5)
+    assert max_threshold == pytest.approx(2.0)
+
+
+def test_get_length_thresholds_3():
+    min_threshold, max_threshold = trycycler.initial_check.get_length_thresholds(1.1)
+    assert min_threshold == pytest.approx(0.909090909090909)
+    assert max_threshold == pytest.approx(1.1)
+
+
+def test_check_length_ratios_1():
+    length_matrix = {('A', 'B'): 1.1, ('B', 'A'): 0.909090909090909,
+                     ('A', 'C'): 1.2, ('C', 'A'): 0.833333333333333,
+                     ('B', 'C'): 1.090909090909091, ('C', 'B'): 0.916666666666667}
+    trycycler.initial_check.check_length_ratios(length_matrix, 1.25)
+
+
+def test_check_length_ratios_2():
+    length_matrix = {('A', 'B'): 1.1, ('B', 'A'): 0.909090909090909,
+                     ('A', 'C'): 1.2, ('C', 'A'): 0.833333333333333,
+                     ('B', 'C'): 1.090909090909091, ('C', 'B'): 0.916666666666667}
+    with pytest.raises(SystemExit):
+        trycycler.initial_check.check_length_ratios(length_matrix, 1.15)
+
+
+def test_check_mash_distances_1():
+    distance_matrix = {('A', 'B'): 0.01, ('B', 'A'): 0.01,
+                       ('A', 'C'): 0.02, ('C', 'A'): 0.02,
+                       ('B', 'C'): 0.03, ('C', 'B'): 0.03}
+    trycycler.initial_check.check_mash_distances(distance_matrix, 0.05)
+
+
+def test_check_mash_distances_2():
+    distance_matrix = {('A', 'B'): 0.01, ('B', 'A'): 0.01,
+                       ('A', 'C'): 0.02, ('C', 'A'): 0.02,
+                       ('B', 'C'): 0.03, ('C', 'B'): 0.03}
+    with pytest.raises(SystemExit):
+        trycycler.initial_check.check_mash_distances(distance_matrix, 0.005)
+
+
+def test_get_length_ratio_matrix():
+    seq_names = ['A', 'B', 'C']
+    seqs = {'A': 'ACGACTCAGACTACGACTAC', 'B': 'ACGACTCAGA', 'C': 'ACGACTCAGACTACGA'}
+    matrix = trycycler.initial_check.get_length_ratio_matrix(seq_names, seqs, 1.5)
+    assert matrix[('A', 'B')] == pytest.approx(2.0)
+    assert matrix[('B', 'A')] == pytest.approx(0.5)
+    assert matrix[('A', 'C')] == pytest.approx(1.25)
+    assert matrix[('C', 'A')] == pytest.approx(0.8)
+    assert matrix[('B', 'C')] == pytest.approx(0.625)
+    assert matrix[('C', 'B')] == pytest.approx(1.6)

trycycler/msa.py

@@ -119,8 +119,9 @@ def check_muscle_results(temp_dir: pathlib.Path, piece_count):
         if not muscle_out_filename.is_file():
             missing_files.append(muscle_out_filename)
     if missing_files:
-        sys.exit(f'Error: MUSCLE failed to complete on {len(missing_files)} of the {piece_count} pieces. Please '
-                 f'remove the most divergent sequences from this cluster and then try again.')
+        sys.exit(f'Error: MUSCLE failed to complete on {len(missing_files)} of the {piece_count} '
+                 f'pieces. Please remove the most divergent sequences from this cluster and then '
+                 f'try again.')
 
 
 def find_next_cutoff_positions(seqs, seq_names, first_seq, seq_positions, kmer_size, step,