def run(options): remover = contam_remover.ContamRemover( options.metadata_tsv, options.bam_in, options.counts_out, options.reads_out_1, options.reads_out_2, contam_out_1=options.contam_out_1, contam_out_2=options.contam_out_2, no_match_out_1=options.no_match_out_1, no_match_out_2=options.no_match_out_2, done_file=options.done_file, ) remover.run()
def test_run_no_match_not_wanted(self): """test run when no_match_are_wanted=False""" metadata_file = os.path.join(data_dir, "run.metadata.tsv") samfile = os.path.join(data_dir, "run.sam") outprefix = "tmp.contam_remover.test_run" counts_file = outprefix + ".counts.tsv" reads1 = outprefix + ".wanted_1.fq" reads2 = outprefix + ".wanted_2.fq" no_match1 = outprefix + ".no_match_1.fq" no_match2 = outprefix + ".no_match_2.fq" contam_1 = outprefix + ".contam_1.fq" contam_2 = outprefix + ".contam_2.fq" done_file = outprefix + ".done" if os.path.exists(done_file): os.unlink(done_file) cremover = contam_remover.ContamRemover( metadata_file, samfile, counts_file, reads1, reads2, contam_out_1=contam_1, contam_out_2=contam_2, no_match_out_1=no_match1, no_match_out_2=no_match2, done_file=done_file, ) cremover.run() for read_type in "contam", "no_match", "wanted": for i in 1, 2: got_file = outprefix + "." + read_type + "_" + str(i) + ".fq" self.assertTrue(os.path.exists(got_file)) expected_file = os.path.join( data_dir, "run.no_match_not_wanted." + read_type + "_" + str(i) + ".fq", ) self.assertTrue( filecmp.cmp(expected_file, got_file, shallow=False)) os.unlink(got_file) expected_counts_file = os.path.join(data_dir, "run.expected_counts.tsv") self.assertTrue( filecmp.cmp(expected_counts_file, counts_file, shallow=False)) os.unlink(counts_file) self.assertTrue(os.path.exists(done_file)) os.unlink(done_file)
def test_run_no_match_not_wanted(self): '''test run when no_match_are_wanted=False''' metadata_file = os.path.join(data_dir, 'run.metadata.tsv') samfile = os.path.join(data_dir, 'run.sam') outprefix = 'tmp.contam_remover.test_run' counts_file = outprefix + '.counts.tsv' reads1 = outprefix + '.wanted_1.fq' reads2 = outprefix + '.wanted_2.fq' no_match1 = outprefix + '.no_match_1.fq' no_match2 = outprefix + '.no_match_2.fq' contam_1 = outprefix + '.contam_1.fq' contam_2 = outprefix + '.contam_2.fq' done_file = outprefix + '.done' if os.path.exists(done_file): os.unlink(done_file) cremover = contam_remover.ContamRemover(metadata_file, samfile, counts_file, reads1, reads2, contam_out_1=contam_1, contam_out_2=contam_2, no_match_out_1=no_match1, no_match_out_2=no_match2, done_file=done_file) cremover.run() for read_type in 'contam', 'no_match', 'wanted': for i in 1, 2: got_file = outprefix + '.' + read_type + '_' + str(i) + '.fq' self.assertTrue(os.path.exists(got_file)) expected_file = os.path.join( data_dir, 'run.no_match_not_wanted.' + read_type + '_' + str(i) + '.fq') self.assertTrue( filecmp.cmp(expected_file, got_file, shallow=False)) os.unlink(got_file) expected_counts_file = os.path.join(data_dir, 'run.expected_counts.tsv') self.assertTrue( filecmp.cmp(expected_counts_file, counts_file, shallow=False)) os.unlink(counts_file) self.assertTrue(os.path.exists(done_file)) os.unlink(done_file)