""" Copyright 2017 Ryan Wick (rrwick@gmail.com) https://github.com/rrwick/Porechop This module contains some tests for Porechop. To run them, execute `python3 -m unittest` from the root Porechop directory. This file is part of Porechop. Porechop 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. Porechop 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 Porechop. If not, see . """ import unittest import os import subprocess import shutil import porechop.misc def get_read_type(filename): _, read_type = porechop.misc.load_fasta_or_fastq(filename) read_type = read_type.lower() compression_type = porechop.misc.get_compression_type(filename) if compression_type == 'plain': return read_type elif compression_type == 'gz': return read_type + '.gz' else: assert False class TestOutputFormat(unittest.TestCase): def run_command(self, command, input_filename): runner_path = os.path.join(os.path.dirname(os.path.dirname(__file__)), 'porechop-runner.py') input_path = os.path.join(os.path.dirname(__file__), input_filename) command = command.replace('porechop', runner_path) command = command.replace('IN', input_path) output_name = 'TEMP_' + str(os.getpid()) command = command.replace('OUT', output_name) try: self.output_file = [x for x in command.split() if output_name in x][0] except IndexError: self.output_file = '' p = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True) out, err = p.communicate() return out.decode(), err.decode() def tearDown(self): if os.path.isfile(self.output_file): os.remove(self.output_file) # The following tests use the auto format and should determine the output type using the output # filename. def test_auto_format_fastq_to_fastq(self): self.run_command('porechop -i IN -o OUT.fastq', 'test_format.fastq') self.assertEqual(get_read_type(self.output_file), 'fastq') def test_auto_format_fastq_to_fastq_gz(self): self.run_command('porechop -i IN -o OUT.fastq.gz', 'test_format.fastq') self.assertEqual(get_read_type(self.output_file), 'fastq.gz') def test_auto_format_fastq_to_fasta(self): self.run_command('porechop -i IN -o OUT.fasta', 'test_format.fastq') self.assertEqual(get_read_type(self.output_file), 'fasta') def test_auto_format_fastq_to_fasta_gz(self): self.run_command('porechop -i IN -o OUT.fasta.gz', 'test_format.fastq') self.assertEqual(get_read_type(self.output_file), 'fasta.gz') def test_auto_format_fastq_to_fastq_gz_weird_caps(self): self.run_command('porechop -i IN -o OUT.fAsTq.Gz', 'test_format.fastq') self.assertEqual(get_read_type(self.output_file), 'fastq.gz') # The following tests use the auto format and pipe to output. They determine the output format # from the input filename, but won't gzip the reads. def test_auto_format_fastq_to_pipe(self): self.run_command('porechop -i IN > OUT', 'test_format.fastq') self.assertEqual(get_read_type(self.output_file), 'fastq') def test_auto_format_fastq_gz_to_pipe(self): self.run_command('porechop -i IN > OUT', 'test_format.fastq.gz') self.assertEqual(get_read_type(self.output_file), 'fastq') def test_auto_format_fasta_to_pipe(self): self.run_command('porechop -i IN > OUT', 'test_format.fasta') self.assertEqual(get_read_type(self.output_file), 'fasta') def test_auto_format_fasta_gz_to_pipe(self): self.run_command('porechop -i IN > OUT', 'test_format.fasta.gz') self.assertEqual(get_read_type(self.output_file), 'fasta') # The following tests explicitly set the output format. def test_explicit_format_fastq_to_fastq(self): self.run_command('porechop -i IN -o OUT --format fastq', 'test_format.fastq') self.assertEqual(get_read_type(self.output_file), 'fastq') def test_explicit_format_fastq_to_fastq_gz(self): self.run_command('porechop -i IN -o OUT --format fastq.gz', 'test_format.fastq') self.assertEqual(get_read_type(self.output_file), 'fastq.gz') def test_explicit_format_fastq_to_fasta(self): self.run_command('porechop -i IN -o OUT --format fasta', 'test_format.fastq') self.assertEqual(get_read_type(self.output_file), 'fasta') def test_explicit_format_fastq_to_fasta_gz(self): self.run_command('porechop -i IN -o OUT --format fasta.gz', 'test_format.fastq') self.assertEqual(get_read_type(self.output_file), 'fasta.gz') def test_explicit_format_fasta_to_fasta(self): self.run_command('porechop -i IN -o OUT --format fasta', 'test_format.fasta') self.assertEqual(get_read_type(self.output_file), 'fasta') def test_explicit_format_fasta_to_fasta_gz(self): self.run_command('porechop -i IN -o OUT --format fasta.gz', 'test_format.fasta') self.assertEqual(get_read_type(self.output_file), 'fasta.gz') # For these tests the output filename conflicts with the requested format. The requested format # should be followed, not the filename. def test_explicit_format_fastq_to_fastq_conflicting_name_1(self): self.run_command('porechop -i IN -o OUT.fasta --format fastq', 'test_format.fastq') self.assertEqual(get_read_type(self.output_file), 'fastq') def test_explicit_format_fastq_to_fastq_conflicting_name_2(self): self.run_command('porechop -i IN -o OUT.fasta.gz --format fastq', 'test_format.fastq.gz') self.assertEqual(get_read_type(self.output_file), 'fastq') def test_explicit_format_fastq_to_fasta_gz_conflicting_name_1(self): self.run_command('porechop -i IN -o OUT.fastq --format fasta.gz', 'test_format.fastq') self.assertEqual(get_read_type(self.output_file), 'fasta.gz') def test_explicit_format_fastq_to_fasta_gz_conflicting_name_2(self): self.run_command('porechop -i IN -o OUT.fastq.gz --format fasta.gz', 'test_format.fasta') self.assertEqual(get_read_type(self.output_file), 'fasta.gz') class TestOutputFormatBarcodes(unittest.TestCase): def run_command(self, command, input_filename): runner_path = os.path.join(os.path.dirname(os.path.dirname(__file__)), 'porechop-runner.py') input_path = os.path.join(os.path.dirname(__file__), input_filename) command = command.replace('porechop', runner_path) command = command.replace('IN', input_path) self.output_dir = 'TEMP_' + str(os.getpid()) command = command.replace('B_DIR', self.output_dir) p = subprocess.Popen(command, stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True) out, err = p.communicate() return out.decode(), err.decode() def tearDown(self): if os.path.isdir(self.output_dir): shutil.rmtree(self.output_dir) def check_output_file_formats(self, output_files, expected_format): for output_file in [os.path.join(self.output_dir, x) for x in output_files]: self.assertTrue(os.path.isfile(output_file)) self.assertEqual(get_read_type(output_file), expected_format) # The following tests use the auto format and should determine the output type using the input # type. def test_auto_format_fastq_to_fastq(self): self.run_command('porechop -i IN -b B_DIR', 'test_format_barcodes.fastq') self.check_output_file_formats(['BC01.fastq', 'BC02.fastq', 'BC03.fastq', 'none.fastq'], 'fastq') def test_auto_format_fastq_gz_to_fastq_gz(self): self.run_command('porechop -i IN -b B_DIR', 'test_format_barcodes.fastq.gz') self.check_output_file_formats(['BC01.fastq.gz', 'BC02.fastq.gz', 'BC03.fastq.gz', 'none.fastq.gz'], 'fastq.gz') def test_auto_format_fasta_to_fasta(self): self.run_command('porechop -i IN -b B_DIR', 'test_format_barcodes.fasta') self.check_output_file_formats(['BC01.fasta', 'BC02.fasta', 'BC03.fasta', 'none.fasta'], 'fasta') def test_auto_format_fasta_gz_to_fasta_gz(self): self.run_command('porechop -i IN -b B_DIR', 'test_format_barcodes.fasta.gz') self.check_output_file_formats(['BC01.fasta.gz', 'BC02.fasta.gz', 'BC03.fasta.gz', 'none.fasta.gz'], 'fasta.gz') # The following tests explicitly set the output format. def test_explicit_format_fastq_to_fastq(self): self.run_command('porechop -i IN -b B_DIR --format fastq', 'test_format_barcodes.fastq') self.check_output_file_formats(['BC01.fastq', 'BC02.fastq', 'BC03.fastq', 'none.fastq'], 'fastq') def test_explicit_format_fastq_to_fastq_gz(self): self.run_command('porechop -i IN -b B_DIR --format fastq.gz', 'test_format_barcodes.fastq') self.check_output_file_formats(['BC01.fastq.gz', 'BC02.fastq.gz', 'BC03.fastq.gz', 'none.fastq.gz'], 'fastq.gz') def test_explicit_format_fastq_gz_to_fastq(self): self.run_command('porechop -i IN -b B_DIR --format fastq', 'test_format_barcodes.fastq.gz') self.check_output_file_formats(['BC01.fastq', 'BC02.fastq', 'BC03.fastq', 'none.fastq'], 'fastq') def test_explicit_format_fastq_gz_to_fastq_gz(self): self.run_command('porechop -i IN -b B_DIR --format fastq.gz', 'test_format_barcodes.fastq.gz') self.check_output_file_formats(['BC01.fastq.gz', 'BC02.fastq.gz', 'BC03.fastq.gz', 'none.fastq.gz'], 'fastq.gz') def test_explicit_format_fastq_to_fasta(self): self.run_command('porechop -i IN -b B_DIR --format fasta', 'test_format_barcodes.fastq') self.check_output_file_formats(['BC01.fasta', 'BC02.fasta', 'BC03.fasta', 'none.fasta'], 'fasta') def test_explicit_format_fastq_to_fasta_gz(self): self.run_command('porechop -i IN -b B_DIR --format fasta.gz', 'test_format_barcodes.fastq') self.check_output_file_formats(['BC01.fasta.gz', 'BC02.fasta.gz', 'BC03.fasta.gz', 'none.fasta.gz'], 'fasta.gz') def test_explicit_format_fasta_to_fasta(self): self.run_command('porechop -i IN -b B_DIR --format fasta', 'test_format_barcodes.fasta') self.check_output_file_formats(['BC01.fasta', 'BC02.fasta', 'BC03.fasta', 'none.fasta'], 'fasta') def test_explicit_format_fasta_to_fasta_gz(self): self.run_command('porechop -i IN -b B_DIR --format fasta.gz', 'test_format_barcodes.fasta') self.check_output_file_formats(['BC01.fasta.gz', 'BC02.fasta.gz', 'BC03.fasta.gz', 'none.fasta.gz'], 'fasta.gz') def test_explicit_format_fasta_gz_to_fasta(self): self.run_command('porechop -i IN -b B_DIR --format fasta', 'test_format_barcodes.fasta.gz') self.check_output_file_formats(['BC01.fasta', 'BC02.fasta', 'BC03.fasta', 'none.fasta'], 'fasta') def test_explicit_format_fasta_gz_to_fasta_gz(self): self.run_command('porechop -i IN -b B_DIR --format fasta.gz', 'test_format_barcodes.fasta.gz') self.check_output_file_formats(['BC01.fasta.gz', 'BC02.fasta.gz', 'BC03.fasta.gz', 'none.fasta.gz'], 'fasta.gz')