Unit tests

.coveragerc

@@ -0,0 +1,2 @@
+[run]
+source = polypolish

polypolish/__main__.py

@@ -20,7 +20,7 @@
 from .help_formatter import MyParser, MyHelpFormatter
 from .log import log, bold, section_header, explanation
 from .polish_targets import polish_target_sequences
-from .misc import get_ascii_art, load_fasta
+from .misc import get_ascii_art, load_fasta, check_python_version
 from .version import __version__
 
 
@@ -31,7 +31,7 @@ def main():
     alignments = load_alignments(args.sam1, args.sam2, args.max_errors)
     new_lengths = polish_target_sequences(alignments, assembly_seqs, args.debug, args.min_depth,
                                           args.min_fraction)
-    finished_message(start_time, new_lengths)
+    finished_message(start_time, new_lengths, args.debug)
 
 
 def parse_args():
@@ -103,7 +103,7 @@ def starting_message(args):
     else:
         log(f'  --debug {args.debug}')
     log()
-    check_python()
+    check_python_version()
     return datetime.datetime.now()
 
 
@@ -133,12 +133,5 @@ def load_assembly(assembly_filename):
     return assembly_seqs
 
 
-def check_python():
-    major, minor = sys.version_info.major, sys.version_info.minor
-    good_version = (major >= 3 and minor >= 6)
-    if not good_version:
-        sys.exit('Error: Polypolish requires Python 3.6 or later')
-
-
 if __name__ == '__main__':
     main()

polypolish/misc.py

@@ -102,3 +102,8 @@ def get_ascii_art():
                  bold_yellow(r"                   __/ || |                             ") + '\n' +
                  bold_yellow(r"                  |___/ |_|                             ") + '\n')
     return ascii_art
+
+
+def check_python_version():
+    if sys.version_info.major < 3 or sys.version_info.minor < 6:
+        sys.exit('\nError: Polypolish requires Python 3.6 or later')

test/test_misc.py

@@ -0,0 +1,145 @@
+"""
+This module contains some tests for Polypolish. To run them, execute `pytest` from the root
+Polypolish directory.
+
+Copyright 2021 Ryan Wick (rrwick@gmail.com)
+https://github.com/rrwick/Polypolish
+
+This file is part of Polypolish. Polypolish 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. Polypolish 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 Polypolish.
+If not, see <http://www.gnu.org/licenses/>.
+"""
+
+import gzip
+import pytest
+import sys
+import unittest.mock
+
+import polypolish.misc
+
+
+def test_get_compression_type_1():
+    assert polypolish.misc.get_compression_type('test/test_misc/test.txt') == 'plain'
+
+
+def test_get_compression_type_2():
+    assert polypolish.misc.get_compression_type('test/test_misc/test.gz') == 'gz'
+
+
+def test_get_compression_type_3():
+    with pytest.raises(SystemExit) as e:
+        polypolish.misc.get_compression_type('test/test_misc/test.bz2')
+    assert 'cannot use bzip2' in str(e.value)
+
+
+def test_get_compression_type_4():
+    with pytest.raises(SystemExit) as e:
+        polypolish.misc.get_compression_type('test/test_misc/test.zip')
+    assert 'cannot use zip' in str(e.value)
+
+
+def test_get_open_func_1():
+    assert polypolish.misc.get_open_func('test/test_misc/test.txt') == open
+
+
+def test_get_open_func_2():
+    assert polypolish.misc.get_open_func('test/test_misc/test.gz') == gzip.open
+
+
+def test_load_fasta_1():
+    seqs = polypolish.misc.load_fasta('test/test_misc/test.fasta')
+    assert len(seqs) == 2
+    assert seqs[0][0] == 'A'
+    assert seqs[0][1].startswith('TTGCCTGTAGTCGGGACC')
+    assert seqs[1][0] == 'B'
+    assert seqs[1][1].startswith('ATTCTCAGAATGGCGTAG')
+
+
+def test_load_fasta_2():
+    seqs = polypolish.misc.load_fasta('test/test_misc/test.fasta', include_full_header=True)
+    assert len(seqs) == 2
+    assert seqs[0][0] == 'A'
+    assert seqs[0][1] == 'A info'
+    assert seqs[0][2].startswith('TTGCCTGTAGTCGGGACC')
+    assert seqs[1][0] == 'B'
+    assert seqs[1][1] == 'B stuff'
+    assert seqs[1][2].startswith('ATTCTCAGAATGGCGTAG')
+
+
+def test_load_fasta_3():
+    seqs = polypolish.misc.load_fasta('test/test_misc/test.fasta.gz')
+    assert len(seqs) == 2
+    assert seqs[0][0] == 'A'
+    assert seqs[0][1].startswith('TTGCCTGTAGTCGGGACC')
+    assert seqs[1][0] == 'B'
+    assert seqs[1][1].startswith('ATTCTCAGAATGGCGTAG')
+
+
+def test_load_fasta_4():
+    seqs = polypolish.misc.load_fasta('test/test_misc/bad_1.fasta')
+    assert len(seqs) == 2
+    assert seqs[0][0] == 'A'
+    assert seqs[0][1].startswith('TTGCCTGTAGTCGGGACC')
+    assert seqs[1][0] == 'B'
+    assert seqs[1][1].startswith('ATTCTCAGAATGGCGTAG')
+
+
+def test_load_fasta_5():
+    seqs = polypolish.misc.load_fasta('test/test_misc/lowercase.fasta')
+    assert len(seqs) == 2
+    assert seqs[0][0] == 'A'
+    assert seqs[0][1].startswith('TTGCCTGTAGTCGGGACC')
+    assert seqs[1][0] == 'B'
+    assert seqs[1][1].startswith('ATTCTCAGAATGGCGTAG')
+
+
+def test_reverse_complement_1():
+    assert polypolish.misc.reverse_complement('GGGGaaaaaaaatttatatat') == 'atatataaattttttttCCCC'
+
+
+def test_reverse_complement_2():
+    assert polypolish.misc.reverse_complement('atatataaattttttttCCCC') == 'GGGGaaaaaaaatttatatat'
+
+
+def test_reverse_complement_3():
+    assert polypolish.misc.reverse_complement('ACGT123') == 'NNNACGT'
+
+
+def test_check_python_version_1():
+    with unittest.mock.patch.object(sys, 'version_info') as v_info:
+        v_info.major = 3
+        v_info.minor = 6
+        polypolish.misc.check_python_version()
+
+
+def test_check_python_version_2():
+    with unittest.mock.patch.object(sys, 'version_info') as v_info:
+        v_info.major = 3
+        v_info.minor = 8
+        polypolish.misc.check_python_version()
+
+
+def test_check_python_version_3():
+    with pytest.raises(SystemExit) as e:
+        with unittest.mock.patch.object(sys, 'version_info') as v_info:
+            v_info.major = 3
+            v_info.minor = 5
+            polypolish.misc.check_python_version()
+    assert 'requires Python 3.6 or later' in str(e.value)
+
+
+def test_check_python_version_4():
+    with pytest.raises(SystemExit) as e:
+        with unittest.mock.patch.object(sys, 'version_info') as v_info:
+            v_info.major = 2
+            v_info.minor = 7
+            polypolish.misc.check_python_version()
+    assert 'requires Python 3.6 or later' in str(e.value)
+
+
+def test_get_ascii_art():
+    assert "| |                     | |(_)     | |" in polypolish.misc.get_ascii_art()

test/test_misc/bad_1.fasta

@@ -0,0 +1,7 @@
+>A
+TTGCCTGTAGTCGGGACCCCGTGACTAGGAAAGCAATCAGCGACTAACAGGCGGAGACCGTCTATAGCGCACGGGGTGTAGTTGGCTATTACTGATCTCT
+
+
+
+>B
+ATTCTCAGAATGGCGTAGTATTCATATTTGTTCGTAGCCCGCCTCCGTACATGTTATTGTGCTCATCGGTGGCCTGCGCCGTGGGGAGTGCAAAACGTGG

test/test_misc/bad_1.fastq

@@ -0,0 +1,9 @@
+@A info
+TTGCCTGTAGTCGGGACCCCGTGACTAGGAAAGCAATCAGCGACTAACAGGCGGAGACCGTCTATAGCGCACGGGGTGTAGTTGGCTATTACTGATCTCT
++
+##$#%#%&++3*&&&-.72:789>;:<74362%&&(%()%$&$$&#(%*'&$%&$%*##$'/-&'&&'%%%'$%#"$#'#$$)##%((#%$('*'$'($'
+
+@B stuff
+ATTCTCAGAATGGCGTAGTATTCATATTTGTTCGTAGCCCGCCTCCGTACATGTTATTGTGCTCATCGGTGGCCTGCGCCGTGGGGAGTGCAAAACGTGG
++
+:;@@AHD98/.5C*-CEC68BHJD/>:@<?>9CA=@??DEIF835<1.*+)<8++1--5?;62<B>9;%3))2/@=BC6651:65.?@>EFBBFNJ@BJK

test/test_misc/bad_2.fastq

@@ -0,0 +1,9 @@
+@A info
+TTGCCTGTAGTCGGGACCCCGTGACTAGGAAAGCAATCAGCGACTAACAGGCGGAGACCGTCTATAGCGCACGGGGTGTAGTTGGCTATTACTGATCTCT
++
+##$#%#%&++3*&&&-.72:789>;:<74362%&&(%()%$&$$&#(%*'&$%&$%*##$'/-&'&&'%%%'$%#"$#'#$$)##%((#%$('*'$'($'
+EXTRA LINE
+@B stuff
+ATTCTCAGAATGGCGTAGTATTCATATTTGTTCGTAGCCCGCCTCCGTACATGTTATTGTGCTCATCGGTGGCCTGCGCCGTGGGGAGTGCAAAACGTGG
++
+:;@@AHD98/.5C*-CEC68BHJD/>:@<?>9CA=@??DEIF835<1.*+)<8++1--5?;62<B>9;%3))2/@=BC6651:65.?@>EFBBFNJ@BJK

test/test_misc/lowercase.fasta

@@ -0,0 +1,4 @@
+>A info
+ttgcctgtagtcgggaccccgtgactaggaaagcaatcagcgactaacaggcggagaccgtctatagcgcacggggtgtagttggctattactgatctct
+>B stuff
+attctcagaatggcgtagtattcatatttgttcgtagcccgcctccgtacatgttattgtgctcatcggtggcctgcgccgtggggagtgcaaaacgtgg

test/test_misc/not_unicode

@@ -0,0 +1 @@
+�vW�l

test/test_misc/test.fasta

@@ -0,0 +1,4 @@
+>A info
+TTGCCTGTAGTCGGGACCCCGTGACTAGGAAAGCAATCAGCGACTAACAGGCGGAGACCGTCTATAGCGCACGGGGTGTAGTTGGCTATTACTGATCTCT
+>B stuff
+ATTCTCAGAATGGCGTAGTATTCATATTTGTTCGTAGCCCGCCTCCGTACATGTTATTGTGCTCATCGGTGGCCTGCGCCGTGGGGAGTGCAAAACGTGG

test/test_misc/test.fastq

@@ -0,0 +1,8 @@
+@A info
+TTGCCTGTAGTCGGGACCCCGTGACTAGGAAAGCAATCAGCGACTAACAGGCGGAGACCGTCTATAGCGCACGGGGTGTAGTTGGCTATTACTGATCTCT
++
+##$#%#%&++3*&&&-.72:789>;:<74362%&&(%()%$&$$&#(%*'&$%&$%*##$'/-&'&&'%%%'$%#"$#'#$$)##%((#%$('*'$'($'
+@B stuff
+ATTCTCAGAATGGCGTAGTATTCATATTTGTTCGTAGCCCGCCTCCGTACATGTTATTGTGCTCATCGGTGGCCTGCGCCGTGGGGAGTGCAAAACGTGG
++
+:;@@AHD98/.5C*-CEC68BHJD/>:@<?>9CA=@??DEIF835<1.*+)<8++1--5?;62<B>9;%3))2/@=BC6651:65.?@>EFBBFNJ@BJK

test/test_misc/test.txt

@@ -0,0 +1 @@
+This is a plain text file.