From 7022e4174549cec9cdfe32c06d6b107c1a06d629 Mon Sep 17 00:00:00 2001
From: Holly Ruess <s185797@biohpcwsc012.biohpc.swmed.edu>
Date: Thu, 26 Dec 2019 10:06:19 -0600
Subject: [PATCH] fix pool and pseudo
---
workflow/scripts/xcor.py | 2 +-
workflow/tests/test_pool_and_psuedoreplicate.py | 15 +++++++++++----
2 files changed, 12 insertions(+), 5 deletions(-)
diff --git a/workflow/scripts/xcor.py b/workflow/scripts/xcor.py
index 8dc4394..8e0dd6b 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 06dae76..f969dfc 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
--
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