Add test for checking overlap of peaks.

workflow/tests/test_overlap_peaks.py

+#!/usr/bin/env python3
+
+import pytest
+import pandas as pd
+from io import StringIO
+import os
+import overlap_peaks
+
+test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
+                '/../output/consensusPeaks/'
+
+DESIGN_STRING = """sample_id\tbam_reads\tbam_index\texperiment_id\tbiosample\tfactor\ttreatment\treplicate\tcontrol_id
+A_1\tA_1.bam\tA_1.bai\tA\tLiver\tH3K27ac\tNone\t1\tB_1
+A_2\tA_2.bam\tA_2.bai\tA\tLiver\tH3K27ac\tNone\t2\tB_2
+B_1\tB_1.bam\tB_1.bai\tB\tLiver\tH3K27ac\tNone\t1\tB_1
+B_2\tB_2.bam\tB_2.bai\tB\tLiver\tH3K27ac\tNone\t2\tB_2
+"""
+
+
+@pytest.fixture
+def design_diff():
+    design_file = StringIO(DESIGN_STRING)
+    design_df = pd.read_csv(design_file, sep="\t")
+    return design_df
+
+
+def test_check_update_design(design_diff):
+    new_design = overlap_peaks.update_design(design_diff)
+    assert df.shape[0] == 2
+    assert new_design.loc[0, 'control_bam_reads'] == "B_1.bam"
+    assert new_design.loc[0, 'peak_caller'] == "bed"
+
+
+def test_overlap_peaks_singleend():
+    assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC.rejected.narrowPeak'))
+    peak_file = test_output_path + 'ENCSR238SGC.replicated.narrowPeak'
+    assert utils.count_lines(peak_file) == '150096'
+
+
+def test_call_peaks_macs_pairedend():
+    # Do the same thing for paired end data
+    pass