From 7bddefc497f64a4c4e64814ad15a493442c8624d Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Mon, 24 Dec 2018 09:29:43 -0600
Subject: [PATCH] Add in paired end test data.
---
workflow/tests/test_map_reads.py | 2 +-
workflow/tests/test_overlap_peaks.py | 7 ++++---
2 files changed, 5 insertions(+), 4 deletions(-)
diff --git a/workflow/tests/test_map_reads.py b/workflow/tests/test_map_reads.py
index 1cb00d3..54948bf 100644
--- a/workflow/tests/test_map_reads.py
+++ b/workflow/tests/test_map_reads.py
@@ -19,7 +19,7 @@ def test_map_reads_singleend():
@pytest.mark.integration
def test_map_reads_pairedend():
assert os.path.exists(os.path.join(test_output_path, 'ENCFF002DTU_val_1ENCFF002EFI_val_2.srt.bam'))
- aligned_reads_report = test_output_path + 'NCFF002DTU_val_1ENCFF002EFI_val_2.srt.bam.flagstat.qc'
+ aligned_reads_report = test_output_path + 'ENCFF002DTU_val_1ENCFF002EFI_val_2.srt.bam.flagstat.qc'
samtools_report = open(aligned_reads_report).readlines()
assert '72660890 + 0 in total' in samtools_report[0]
assert '72053925 + 0 mapped (99.16% : N/A)' in samtools_report[4]
diff --git a/workflow/tests/test_overlap_peaks.py b/workflow/tests/test_overlap_peaks.py
index f75ebcd..ce83540 100644
--- a/workflow/tests/test_overlap_peaks.py
+++ b/workflow/tests/test_overlap_peaks.py
@@ -41,6 +41,7 @@ def test_overlap_peaks_singleend():
@pytest.mark.integration
-def test_call_peaks_macs_pairedend():
- # Do the same thing for paired end data
- pass
+def test_overlap_peaks_pairedend():
+ assert os.path.exists(os.path.join(test_output_path, 'ENCSR729LGA.rejected.narrowPeak'))
+ peak_file = test_output_path + 'ENCSR729LGA.replicated.narrowPeak'
+ assert utils.count_lines(peak_file) == 25655
--
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