From 58b92f5deecea0ca512d04e129e07ba5daa15697 Mon Sep 17 00:00:00 2001 From: Venkat Malladi <venkat.malladi@utsouthwestern.edu> Date: Sat, 11 Aug 2018 20:09:45 -0500 Subject: [PATCH] Add in paired-end filter test. --- workflow/tests/test_map_qc.py | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/workflow/tests/test_map_qc.py b/workflow/tests/test_map_qc.py index a882e53..f2c4e74 100644 --- a/workflow/tests/test_map_qc.py +++ b/workflow/tests/test_map_qc.py @@ -25,5 +25,14 @@ def test_map_qc_singleend(): @pytest.mark.integration def test_map_qc_pairedend(): - # Do the same thing for paired end data - pass + assert os.path.exists(os.path.join(test_output_path, 'ENCFF293YFE_val_2ENCFF330MCZ_val_1.filt.nodup.bam')) + assert os.path.exists(os.path.join(test_output_path, 'ENCFF293YFE_val_2ENCFF330MCZ_val_1.filt.nodup.bambai')) + filtered_reads_report = test_output_path + 'ENCFF293YFE_val_2ENCFF330MCZ_val_1.filt.nodup.flagstat.qc' + samtools_report = open(filtered_reads_report).readlines() + assert '47389080 + 0 in total' in samtools_report[0] + assert '47389080 + 0 mapped (100.00%:N/A)' in samtools_report[4] + library_complexity = test_output_path + 'ENCFF293YFE_val_2ENCFF330MCZ_val_1.filt.nodup.pbc.qc' + df_library_complexity = pd.read_csv(library_complexity, sep='\t') + assert df_library_complexity["NRF"].iloc[0] == 0.947064 + assert df_library_complexity["PBC1"].iloc[0] == 0.946724 + assert df_library_complexity["PBC2"].iloc[0] == 18.643039 -- GitLab