def test_w_sample_metadata(self): df = pd.DataFrame({'Subject': ['subject-1', 'subject-1', 'subject-2'], 'SampleType': ['gut', 'tongue', 'gut']}, index=pd.Index(['S1', 'S2', 'S3'], name='id')) metadata = qiime2.Metadata(df) table = biom.Table(np.array([[0, 1, 3], [1, 1, 2]]), ['O1', 'O2'], ['S1', 'S2', 'S3']) with tempfile.TemporaryDirectory() as output_dir: summarize(output_dir, table, metadata) index_fp = os.path.join(output_dir, 'index.html') self.assertTrue(os.path.exists(index_fp)) feature_freq_fp = os.path.join(output_dir, 'feature-frequency-detail.csv') self.assertTrue(os.path.exists(feature_freq_fp)) self.assertTrue('O1,4' in open(feature_freq_fp).read()) sample_freq_fp = os.path.join(output_dir, 'sample-frequency-detail.csv') self.assertTrue(os.path.exists(sample_freq_fp)) self.assertTrue('S1,1' in open(sample_freq_fp).read()) interactive_sample_detail_fp = \ os.path.join(output_dir, 'data.jsonp') self.assertTrue(os.path.exists(interactive_sample_detail_fp)) self.assertTrue('SampleType' in open(interactive_sample_detail_fp).read())
def test_basic(self): table = biom.Table(np.array([[0, 1, 3], [1, 1, 2], [400, 450, 500], [1000, 10000, 100000], [52, 42, 99]]), ['O1', 'O2', '03', '04', 'O5'], ['S1', 'S2', 'S3']) with tempfile.TemporaryDirectory() as output_dir: summarize(output_dir, table) index_fp = os.path.join(output_dir, 'index.html') self.assertTrue(os.path.exists(index_fp)) feature_freq_fp = os.path.join(output_dir, 'feature-frequency-detail.csv') self.assertTrue(os.path.exists(feature_freq_fp)) self.assertTrue('O1,4' in open(feature_freq_fp).read()) sample_freq_fp = os.path.join(output_dir, 'sample-frequency-detail.csv') self.assertTrue(os.path.exists(sample_freq_fp)) self.assertTrue('S1,1453' in open(sample_freq_fp).read()) interactive_sample_detail_fp = \ os.path.join(output_dir, 'data.jsonp') self.assertTrue(os.path.exists(interactive_sample_detail_fp))
def test_basic(self): table = biom.Table(np.array([[0, 1, 3], [1, 1, 2], [400, 450, 500], [1000, 10000, 100000], [52, 42, 99]]), ['O1', 'O2', '03', '04', 'O5'], ['S1', 'S2', 'S3']) with tempfile.TemporaryDirectory() as output_dir: summarize(output_dir, table) index_fp = os.path.join(output_dir, 'index.html') self.assertTrue(os.path.exists(index_fp)) feature_freq_fp = os.path.join(output_dir, 'feature-frequency-detail.csv') self.assertTrue(os.path.exists(feature_freq_fp)) self.assertTrue('O1,4' in open(feature_freq_fp).read()) sample_freq_fp = os.path.join(output_dir, 'sample-frequency-detail.csv') self.assertTrue(os.path.exists(sample_freq_fp)) self.assertTrue('S1,1453' in open(sample_freq_fp).read()) interactive_sample_detail_fp = \ os.path.join(output_dir, 'data.jsonp') self.assertTrue(os.path.exists(interactive_sample_detail_fp))
def test_w_sample_metadata(self): df = pd.DataFrame({'Subject': ['subject-1', 'subject-1', 'subject-2'], 'SampleType': ['gut', 'tongue', 'gut']}, index=pd.Index(['S1', 'S2', 'S3'], name='id')) metadata = qiime2.Metadata(df) table = biom.Table(np.array([[0, 1, 3], [1, 1, 2]]), ['O1', 'O2'], ['S1', 'S2', 'S3']) with tempfile.TemporaryDirectory() as output_dir: summarize(output_dir, table, metadata) index_fp = os.path.join(output_dir, 'index.html') self.assertTrue(os.path.exists(index_fp)) feature_freq_fp = os.path.join(output_dir, 'feature-frequency-detail.csv') self.assertTrue(os.path.exists(feature_freq_fp)) self.assertTrue('O1,4' in open(feature_freq_fp).read()) sample_freq_fp = os.path.join(output_dir, 'sample-frequency-detail.csv') self.assertTrue(os.path.exists(sample_freq_fp)) self.assertTrue('S1,1' in open(sample_freq_fp).read()) interactive_sample_detail_fp = \ os.path.join(output_dir, 'data.jsonp') self.assertTrue(os.path.exists(interactive_sample_detail_fp)) self.assertTrue('SampleType' in open(interactive_sample_detail_fp).read())
def test_one_sample(self): sample_frequencies_pdf_fn = 'sample-frequencies.pdf' # sample-frequencies.pdf should not be written when there is only # one sample... table = biom.Table(np.array([[0], [1]]), ['O1', 'O2'], ['S1']) with tempfile.TemporaryDirectory() as output_dir: summarize(output_dir, table) sample_frequencies_pdf_fp = \ os.path.join(output_dir, sample_frequencies_pdf_fn) self.assertFalse(os.path.exists(sample_frequencies_pdf_fp)) # but it should be written when there is more than one sample table = biom.Table(np.array([[0, 1, 3], [1, 1, 2]]), ['O1', 'O2'], ['S1', 'S2', 'S3']) with tempfile.TemporaryDirectory() as output_dir: summarize(output_dir, table) sample_frequencies_pdf_fp = \ os.path.join(output_dir, sample_frequencies_pdf_fn) self.assertTrue(os.path.exists(sample_frequencies_pdf_fp))
def test_frequency_ranges_are_zero(self): table = biom.Table(np.array([[25, 25, 25], [25, 25, 25]]), ['O1', 'O2'], ['S1', 'S2', 'S3']) with tempfile.TemporaryDirectory() as output_dir: summarize(output_dir, table) index_fp = os.path.join(output_dir, 'index.html') self.assertTrue(os.path.exists(index_fp)) feature_freq_fp = os.path.join(output_dir, 'feature-frequency-detail.csv') self.assertTrue(os.path.exists(feature_freq_fp)) self.assertTrue('O1,75' in open(feature_freq_fp).read()) sample_freq_fp = os.path.join(output_dir, 'sample-frequency-detail.csv') self.assertTrue(os.path.exists(sample_freq_fp)) self.assertTrue('S1,50' in open(sample_freq_fp).read())
def test_one_sample(self): sample_frequencies_pdf_fn = 'sample-frequencies.pdf' # sample-frequencies.pdf should not be written when there is only # one sample... table = biom.Table(np.array([[0], [1]]), ['O1', 'O2'], ['S1']) with tempfile.TemporaryDirectory() as output_dir: summarize(output_dir, table) sample_frequencies_pdf_fp = \ os.path.join(output_dir, sample_frequencies_pdf_fn) self.assertFalse(os.path.exists(sample_frequencies_pdf_fp)) # but it should be written when there is more than one sample table = biom.Table(np.array([[0, 1, 3], [1, 1, 2]]), ['O1', 'O2'], ['S1', 'S2', 'S3']) with tempfile.TemporaryDirectory() as output_dir: summarize(output_dir, table) sample_frequencies_pdf_fp = \ os.path.join(output_dir, sample_frequencies_pdf_fn) self.assertTrue(os.path.exists(sample_frequencies_pdf_fp))
def test_frequency_ranges_are_zero(self): table = biom.Table(np.array([[25, 25, 25], [25, 25, 25]]), ['O1', 'O2'], ['S1', 'S2', 'S3']) with tempfile.TemporaryDirectory() as output_dir: summarize(output_dir, table) index_fp = os.path.join(output_dir, 'index.html') self.assertTrue(os.path.exists(index_fp)) feature_freq_fp = os.path.join(output_dir, 'feature-frequency-detail.csv') self.assertTrue(os.path.exists(feature_freq_fp)) self.assertTrue('O1,75' in open(feature_freq_fp).read()) sample_freq_fp = os.path.join(output_dir, 'sample-frequency-detail.csv') self.assertTrue(os.path.exists(sample_freq_fp)) self.assertTrue('S1,50' in open(sample_freq_fp).read()) interactive_sample_detail_fp = \ os.path.join(output_dir, 'data.jsonp') self.assertTrue(os.path.exists(interactive_sample_detail_fp))