From d84a3b62089c24a748e1297065456b1807f15e3b Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Thu, 27 Dec 2018 08:29:15 -0600
Subject: [PATCH] Check differential peaks.
---
.gitlab-ci.yml | 4 +--
workflow/tests/test_diff_peaks.py | 48 +++++++++++++++++++++++++++++++
2 files changed, 50 insertions(+), 2 deletions(-)
create mode 100644 workflow/tests/test_diff_peaks.py
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 99d55cb..60a430b 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -35,7 +35,7 @@ single_end_diff:
stage: integration
script:
- nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' -resume
- - pytest -m pairedend
+ - pytest -m singlediff
- pytest --cov=./workflow/scripts
artifacts:
expire_in: 2 days
@@ -44,7 +44,7 @@ paired_end_diff:
stage: integration
script:
- nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_PE.txt" --genome 'GRCh38' --pairedEnd true -resume
- - pytest -m pairedend
+ - pytest -m paireddiff
- pytest --cov=./workflow/scripts
artifacts:
expire_in: 2 days
diff --git a/workflow/tests/test_diff_peaks.py b/workflow/tests/test_diff_peaks.py
new file mode 100644
index 0000000..6b4a6ed
--- /dev/null
+++ b/workflow/tests/test_diff_peaks.py
@@ -0,0 +1,48 @@
+#!/usr/bin/env python3
+
+import pytest
+import pandas as pd
+from io import StringIO
+import os
+import utils
+
+test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
+ '/../output/diffPeaks/'
+
+
+@pytest.mark.singleend
+def test_diff_peaks_singleend_single_rep():
+ assert os.path.exists(os.path.join(test_output_path, 'no_diffbind.bed'))
+ assert os.path.exists(os.path.join(test_output_path, 'no_diffbind.csv'))
+ assert os.path.exists(os.path.join(test_output_path, 'no_heatmap.pdf'))
+ assert os.path.exists(os.path.join(test_output_path, 'no_pca.pdf'))
+ assert os.path.exists(os.path.join(test_output_path, 'normcount_peaksets.pdf'))
+
+
+@pytest.mark.pairedend
+def test_annotate_peaks_pairedend_single_rep():
+ assert os.path.exists(os.path.join(test_output_path, 'no_diffbind.bed'))
+ assert os.path.exists(os.path.join(test_output_path, 'no_diffbind.csv'))
+ assert os.path.exists(os.path.join(test_output_path, 'no_heatmap.pdf'))
+ assert os.path.exists(os.path.join(test_output_path, 'no_pca.pdf'))
+ assert os.path.exists(os.path.join(test_output_path, 'normcount_peaksets.pdf'))
+
+@pytest.mark.singlediff
+def test_diff_peaks_singleend_multiple_rep():
+ assert os.path.exists(os.path.join(test_output_path, 'heatmap.pdf'))
+ assert os.path.exists(os.path.join(test_output_path, 'pca.pdf'))
+ assert os.path.exists(os.path.join(test_output_path, 'normcount_peaksets.txt'))
+ assert os.path.exists(os.path.join(test_output_path, 'ENCSR272GNQ_vs_ENCSR238SGC_diffbind.bed'))
+ diffbind_file = test_output_path + 'ENCSR272GNQ_vs_ENCSR238SGC_diffbind.csv'
+ assert os.path.exists(diffbind_file)
+ assert utils.count_lines(diffbind_file) == 201039
+
+@pytest.mark.paireddiff
+def test_annotate_peaks_pairedend_single_rep():
+ assert os.path.exists(os.path.join(test_output_path, 'heatmap.pdf'))
+ assert os.path.exists(os.path.join(test_output_path, 'pca.pdf'))
+ assert os.path.exists(os.path.join(test_output_path, 'normcount_peaksets.txt'))
+ assert os.path.exists(os.path.join(test_output_path, 'ENCSR729LGA_vs_ENCSR757EMK_diffbind.bed'))
+ diffbind_file = test_output_path + 'ENCSR729LGA_vs_ENCSR757EMK_diffbind.csv'
+ assert os.path.exists(diffbind_file)
+ assert utils.count_lines(diffbind_file) == 112652
--
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