From 89340f9c4767f9f18daf41fe3a61c320fcea73d0 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Tue, 15 Jan 2019 09:29:46 -0600
Subject: [PATCH] Modify tests.
---
workflow/tests/test_annotate_peaks.py | 4 ++--
workflow/tests/test_call_peaks_macs.py | 6 +++---
workflow/tests/test_map_qc.py | 4 ++--
workflow/tests/test_overlap_peaks.py | 4 ++--
workflow/tests/test_trim_reads.py | 6 +++---
workflow/tests/test_xcor.py | 6 +++---
6 files changed, 15 insertions(+), 15 deletions(-)
diff --git a/workflow/tests/test_annotate_peaks.py b/workflow/tests/test_annotate_peaks.py
index 692ddce..4608f66 100644
--- a/workflow/tests/test_annotate_peaks.py
+++ b/workflow/tests/test_annotate_peaks.py
@@ -16,7 +16,7 @@ def test_annotate_peaks_singleend():
assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC.chipseeker_upsetplot.pdf'))
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) == 149820
@pytest.mark.pairedend
@@ -25,4 +25,4 @@ def test_annotate_peaks_pairedend():
assert os.path.exists(os.path.join(test_output_path, 'ENCSR729LGA.chipseeker_upsetplot.pdf'))
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) == 25579
diff --git a/workflow/tests/test_call_peaks_macs.py b/workflow/tests/test_call_peaks_macs.py
index dabfd71..628a914 100644
--- a/workflow/tests/test_call_peaks_macs.py
+++ b/workflow/tests/test_call_peaks_macs.py
@@ -12,7 +12,7 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
def test_call_peaks_macs_singleend():
assert os.path.exists(os.path.join(test_output_path, 'ENCLB144FDT.fc_signal.bw'))
assert os.path.exists(os.path.join(test_output_path, 'ENCLB144FDT.pvalue_signal.bw'))
- assert os.path.exists(os.path.join(test_output_path, 'ENCLB144FDT.xls'))
+ assert os.path.exists(os.path.join(test_output_path, 'ENCLB144FDT_peaks.xls'))
peak_file = test_output_path + 'ENCLB144FDT.narrowPeak'
assert utils.count_lines(peak_file) == 227389
@@ -21,6 +21,6 @@ def test_call_peaks_macs_singleend():
def test_call_peaks_macs_pairedend():
assert os.path.exists(os.path.join(test_output_path, 'ENCLB568IYX.fc_signal.bw'))
assert os.path.exists(os.path.join(test_output_path, 'ENCLB568IYX.pvalue_signal.bw'))
- assert os.path.exists(os.path.join(test_output_path, 'ENCLB568IYX.xls'))
+ assert os.path.exists(os.path.join(test_output_path, 'ENCLB568IYX_peak.xls'))
peak_file = test_output_path + 'ENCLB568IYX.narrowPeak'
- assert utils.count_lines(peak_file) == 112652
+ assert utils.count_lines(peak_file) == 113821
diff --git a/workflow/tests/test_map_qc.py b/workflow/tests/test_map_qc.py
index 5ae8218..1c0d23e 100644
--- a/workflow/tests/test_map_qc.py
+++ b/workflow/tests/test_map_qc.py
@@ -31,8 +31,8 @@ def test_map_qc_pairedend():
assert os.path.exists(os.path.join(test_output_path, 'ENCLB568IYX.dedup.qc'))
filtered_reads_report = test_output_path + 'ENCLB568IYX.dedup.flagstat.qc'
samtools_report = open(filtered_reads_report).readlines()
- assert '47389080 + 0 in total' in samtools_report[0]
- assert '47389080 + 0 mapped (100.00%:N/A)' in samtools_report[4]
+ assert '47388510 + 0 in total' in samtools_report[0]
+ assert '47388510 + 0 mapped (100.00%:N/A)' in samtools_report[4]
library_complexity = test_output_path + 'ENCLB568IYX.pbc.qc'
df_library_complexity = pd.read_csv(library_complexity, sep='\t')
assert df_library_complexity["NRF"].iloc[0] == 0.947064
diff --git a/workflow/tests/test_overlap_peaks.py b/workflow/tests/test_overlap_peaks.py
index 99d43b8..63d4752 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) == 149828
@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) == 25655
+ assert utils.count_lines(peak_file) == 25847
diff --git a/workflow/tests/test_trim_reads.py b/workflow/tests/test_trim_reads.py
index 680f237..dd3f779 100644
--- a/workflow/tests/test_trim_reads.py
+++ b/workflow/tests/test_trim_reads.py
@@ -13,7 +13,7 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
@pytest.mark.singleend
def test_trim_reads_singleend():
raw_fastq = test_data_path + 'ENCFF833BLU.fastq.gz'
- trimmed_fastq = test_output_path + 'ENCLB144FDT_R1.fq.gz'
+ trimmed_fastq = test_output_path + 'ENCLB144FDT_R1_trimmed.fq.gz'
trimmed_fastq_report = test_output_path + \
'ENCLB144FDT_R1_trimmed.fq.gz_trimming_report.txt'
assert os.path.getsize(raw_fastq) != os.path.getsize(trimmed_fastq)
@@ -24,9 +24,9 @@ def test_trim_reads_singleend():
@pytest.mark.pairedend
def test_trim_reads_pairedend():
raw_fastq = test_data_path + 'ENCFF582IOZ.fastq.gz'
- trimmed_fastq = test_output_path + 'ENCLB637LZP_R2.fq.gz'
+ trimmed_fastq = test_output_path + 'ENCLB637LZP_R2_val_2.fq.gz'
trimmed_fastq_report = test_output_path + \
- 'ENCLB637LZP_R2_val_2.fq.gz_trimming_report.txt'
+ 'ENCLB637LZP_R2.fastq.gz_trimming_report.txt'
assert os.path.getsize(raw_fastq) != os.path.getsize(trimmed_fastq)
assert os.path.getsize(trimmed_fastq) == 2229312710
assert 'Trimming mode: paired-end' in open(trimmed_fastq_report).readlines()[4]
diff --git a/workflow/tests/test_xcor.py b/workflow/tests/test_xcor.py
index 40548cf..c408c98 100644
--- a/workflow/tests/test_xcor.py
+++ b/workflow/tests/test_xcor.py
@@ -23,6 +23,6 @@ def test_cross_pairedend():
assert os.path.exists(os.path.join(test_output_path, 'ENCLB568IYX.cc.plot.pdf'))
qc_file = os.path.join(test_output_path,"ENCLB568IYX.cc.qc")
df_xcor = pd.read_csv(qc_file, sep="\t", header=None)
- assert df_xcor[2].iloc[0] == '210,220,475'
- assert round(df_xcor[8].iloc[0],6) == 1.062032
- assert df_xcor[9].iloc[0] == 3.737722
+ assert df_xcor[2].iloc[0] == '220,430,475'
+ assert round(df_xcor[8].iloc[0],6) == 1.060018
+ assert df_xcor[9].iloc[0] == 4.099357
--
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