From 6f79eba43fd319dfda551dc3a0abe9f4aecfcc0d Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Fri, 8 Mar 2019 07:04:21 -0600
Subject: [PATCH] Fix test output.
---
workflow/tests/test_annotate_peaks.py | 4 ++--
workflow/tests/test_call_peaks_macs.py | 2 +-
workflow/tests/test_experiment_qc.py | 20 ++++++++++----------
workflow/tests/test_map_qc.py | 2 +-
workflow/tests/test_overlap_peaks.py | 4 ++--
workflow/tests/test_trim_reads.py | 2 +-
6 files changed, 17 insertions(+), 17 deletions(-)
diff --git a/workflow/tests/test_annotate_peaks.py b/workflow/tests/test_annotate_peaks.py
index ef42a9a..ee3ebe1 100644
--- a/workflow/tests/test_annotate_peaks.py
+++ b/workflow/tests/test_annotate_peaks.py
@@ -23,7 +23,7 @@ def test_upsetplot_singleend():
def test_annotation_singleend():
annotation_file = test_output_path + 'ENCSR238SGC.chipseeker_annotation.tsv'
assert os.path.exists(annotation_file)
- assert utils.count_lines(annotation_file) == 152840
+ assert utils.count_lines(annotation_file) == 152255
@pytest.mark.pairedend
@@ -40,4 +40,4 @@ def test_upsetplot_pairedend():
def test_annotation_pairedend():
annotation_file = test_output_path + 'ENCSR729LGA.chipseeker_annotation.tsv'
assert os.path.exists(annotation_file)
- assert utils.count_lines(annotation_file) == 25391
+ assert utils.count_lines(annotation_file) == 25494
diff --git a/workflow/tests/test_call_peaks_macs.py b/workflow/tests/test_call_peaks_macs.py
index 91c1d0e..9f3f6c0 100644
--- a/workflow/tests/test_call_peaks_macs.py
+++ b/workflow/tests/test_call_peaks_macs.py
@@ -41,7 +41,7 @@ def test_pvalue_signal_pairedend():
@pytest.mark.pairedend
def test_peaks_xls_pairedend():
- assert os.path.exists(os.path.join(test_output_path, 'ENCLB568IYX_peak.xls'))
+ assert os.path.exists(os.path.join(test_output_path, 'ENCLB568IYX_peaks.xls'))
@pytest.mark.pairedend
diff --git a/workflow/tests/test_experiment_qc.py b/workflow/tests/test_experiment_qc.py
index 17f8eaa..c0cd5d7 100644
--- a/workflow/tests/test_experiment_qc.py
+++ b/workflow/tests/test_experiment_qc.py
@@ -33,42 +33,42 @@ def test_check_update_controls(design_bam):
@pytest.mark.singleend
def test_coverage_singleend():
assert os.path.exists(os.path.join(test_output_path, 'sample_mbs.npz'))
- assert os.path.exists(os.path.join(test_output_path, 'coverage.png'))
+ assert os.path.exists(os.path.join(test_output_path, 'coverage.pdf'))
@pytest.mark.singleend
def test_spearman_singleend():
- assert os.path.exists(os.path.join(test_output_path, 'heatmap_SpearmanCorr.png'))
+ assert os.path.exists(os.path.join(test_output_path, 'heatmap_SpearmanCorr.pdf'))
@pytest.mark.singleend
def test_pearson_singleend():
- assert os.path.exists(os.path.join(test_output_path, 'heatmap_PearsonCorr.png'))
+ assert os.path.exists(os.path.join(test_output_path, 'heatmap_PearsonCorr.pdf'))
@pytest.mark.singleend
def test_fingerprint_singleend():
- assert os.path.exists(os.path.join(test_output_path, 'ENCLB144FDT_fingerprint.png'))
- assert os.path.exists(os.path.join(test_output_path, 'ENCLB831RUI_fingerprint.png'))
+ assert os.path.exists(os.path.join(test_output_path, 'ENCLB144FDT_fingerprint.pdf'))
+ assert os.path.exists(os.path.join(test_output_path, 'ENCLB831RUI_fingerprint.pdf'))
@pytest.mark.pairdend
def test_coverage_pairedend():
assert os.path.exists(os.path.join(test_output_path, 'sample_mbs.npz'))
- assert os.path.exists(os.path.join(test_output_path, 'coverage.png'))
+ assert os.path.exists(os.path.join(test_output_path, 'coverage.pdf'))
@pytest.mark.pairdend
def test_spearman_pairedend():
- assert os.path.exists(os.path.join(test_output_path, 'heatmap_SpearmanCorr.png'))
+ assert os.path.exists(os.path.join(test_output_path, 'heatmap_SpearmanCorr.pdf'))
@pytest.mark.pairdend
def test_pearson_pairedend():
- assert os.path.exists(os.path.join(test_output_path, 'heatmap_PearsonCorr.png'))
+ assert os.path.exists(os.path.join(test_output_path, 'heatmap_PearsonCorr.pdf'))
@pytest.mark.pairdend
def test_fingerprint_pairedend():
- assert os.path.exists(os.path.join(test_output_path, 'ENCLB568IYX_fingerprint.png'))
- assert os.path.exists(os.path.join(test_output_path, 'ENCLB637LZP_fingerprint.png'))
+ assert os.path.exists(os.path.join(test_output_path, 'ENCLB568IYX_fingerprint.pdf'))
+ assert os.path.exists(os.path.join(test_output_path, 'ENCLB637LZP_fingerprint.pdf'))
diff --git a/workflow/tests/test_map_qc.py b/workflow/tests/test_map_qc.py
index 7bff060..5a94421 100644
--- a/workflow/tests/test_map_qc.py
+++ b/workflow/tests/test_map_qc.py
@@ -53,4 +53,4 @@ def test_library_complexity_pairedend():
df_library_complexity = pd.read_csv(library_complexity, sep='\t')
assert df_library_complexity["NRF"].iloc[0] == 0.947064
assert round(df_library_complexity["PBC1"].iloc[0],6) == 0.946723
- assert df_library_complexity["PBC2"].iloc[0] == 18.643039
+ assert round(df_library_complexity["PBC2"].iloc[0],6) == 18.642645
diff --git a/workflow/tests/test_overlap_peaks.py b/workflow/tests/test_overlap_peaks.py
index 9289d16..ff61c93 100644
--- a/workflow/tests/test_overlap_peaks.py
+++ b/workflow/tests/test_overlap_peaks.py
@@ -37,11 +37,11 @@ def test_check_update_design(design_diff):
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) == 152848
+ assert utils.count_lines(peak_file) == 152262
@pytest.mark.pairedend
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) == 26281
+ assert utils.count_lines(peak_file) == 25758
diff --git a/workflow/tests/test_trim_reads.py b/workflow/tests/test_trim_reads.py
index f929d9c..ca25db6 100644
--- a/workflow/tests/test_trim_reads.py
+++ b/workflow/tests/test_trim_reads.py
@@ -21,7 +21,7 @@ def test_trim_reads_singleend():
@pytest.mark.singleend
def test_trim_report_singleend():
trimmed_fastq_report = test_output_path + \
- 'ENCLB144FDT_R1_trimmed.fq.gz_trimming_report.txt'
+ 'ENCLB144FDT_R1.fastq.gz_trimming_report.txt'
assert 'Trimming mode: single-end' in open(trimmed_fastq_report).readlines()[4]
--
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