diff --git a/workflow/scripts/xcor.py b/workflow/scripts/xcor.py index 8dc4394d3af768e47fa8314549634ddb1a23bd9b..8e0dd6b081fce791f6634759416067e194fbc03f 100644 --- a/workflow/scripts/xcor.py +++ b/workflow/scripts/xcor.py @@ -102,7 +102,7 @@ def xcor(tag, paired): # Subsample tagAlign file number_reads = 15000000 subsampled_tag_filename = \ - tag_basename + ".%d.tagAlign.gz" % (numReads/1000000) + tag_basename + ".%d.tagAlign.gz" % (number_reads/1000000) steps = [ 'zcat %s' % (tag), diff --git a/workflow/tests/test_pool_and_psuedoreplicate.py b/workflow/tests/test_pool_and_psuedoreplicate.py index 06dae76b7ae2906d87d7f19bde9909f99027d507..f969dfcb6f819e8d41d2792fb33e7c8c1ab6587c 100644 --- a/workflow/tests/test_pool_and_psuedoreplicate.py +++ b/workflow/tests/test_pool_and_psuedoreplicate.py @@ -41,15 +41,22 @@ def test_check_replicates_single(design_experiment_2): assert no_reps == 1 -@pytest.mark.integration -def test_pool_and_psuedoreplicate_single_end(): +@pytest.mark.singleend_human +def test_pool_and_psuedoreplicate_singleend_human(): design_file = os.path.join(test_output_path, 'ENCSR265ZXX_ppr.tsv') assert os.path.exists(design_file) design_df = pd.read_csv(design_file, sep="\t") assert design_df.shape[0] == 6 -@pytest.mark.integration -def test_experiment_design_paired_end(): +@pytest.mark.pairedend_mouse +def test_experiment_design_pairedend_mouse(): # Do the same thing for paired end data pass + +@pytest.mark.pairedend_mouse +def test_pool_and_psuedoreplicate_pairedend_mouse(): + design_file = os.path.join(test_output_path, 'ENCSR451NAE_ppr.tsv') + assert os.path.exists(design_file) + design_df = pd.read_csv(design_file, sep="\t") + assert design_df.shape[0] == 5