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Commit 2f1c6283 authored by Venkat Malladi's avatar Venkat Malladi
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Fix tests.

parent 51489c2c
1 merge request!22Resolve "New folders for all steps"
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workflow/tests/test_convert_reads.py
+ 4
− 4
View file @ 2f1c6283
...@@ -9,19 +9,19 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \ ...@@ -9,19 +9,19 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
@pytest.mark.singleend @pytest.mark.singleend
def test_tag_reads_singleend(): def test_tag_reads_singleend():
assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC/ENCLB831RUI.tagAlign.gz')) assert os.path.exists(os.path.join(test_output_path, 'ENCLB831RUI/ENCLB831RUI.tagAlign.gz'))
@pytest.mark.singleend @pytest.mark.singleend
def test_bed_reads_singleend(): def test_bed_reads_singleend():
assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC/ENCLB831RUI.bedse.gz')) assert os.path.exists(os.path.join(test_output_path, 'ENCLB831RUI/ENCLB831RUI.bedse.gz'))
@pytest.mark.pairedend @pytest.mark.pairedend
def test_tag_reads_pairedend(): def test_tag_reads_pairedend():
assert os.path.exists(os.path.join(test_output_path, 'ENCSR729LGA/ENCLB568IYX.tagAlign.gz')) assert os.path.exists(os.path.join(test_output_path, 'ENCLB568IYX/ENCLB568IYX.tagAlign.gz'))
@pytest.mark.pairedend @pytest.mark.pairedend
def test_bed_reads_pairedend(): def test_bed_reads_pairedend():
assert os.path.exists(os.path.join(test_output_path, 'ENCSR729LGA/ENCLB568IYX.bedpe.gz')) assert os.path.exists(os.path.join(test_output_path, 'ENCLB568IYX/ENCLB568IYX.bedpe.gz'))
workflow/tests/test_map_qc.py
+ 10
− 10
View file @ 2f1c6283
...@@ -10,14 +10,14 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \ ...@@ -10,14 +10,14 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
@pytest.mark.singleend @pytest.mark.singleend
def test_dedup_files_singleend(): def test_dedup_files_singleend():
assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC/ENCLB831RUI.dedup.bam')) assert os.path.exists(os.path.join(test_output_path, 'ENCLB831RUI/ENCLB831RUI.dedup.bam'))
assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC/ENCLB831RUI.dedup.bam.bai')) assert os.path.exists(os.path.join(test_output_path, 'ENCLB831RUI/ENCLB831RUI.dedup.bam.bai'))
assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC/ENCLB831RUI.dedup.qc')) assert os.path.exists(os.path.join(test_output_path, 'ENCLB831RUI/ENCLB831RUI.dedup.qc'))
@pytest.mark.singleend @pytest.mark.singleend
def test_map_qc_singleend(): def test_map_qc_singleend():
filtered_reads_report = test_output_path + 'ENCSR238SGC/ENCLB831RUI.dedup.flagstat.qc' filtered_reads_report = test_output_path + 'ENCLB831RUI/ENCLB831RUI.dedup.flagstat.qc'
samtools_report = open(filtered_reads_report).readlines() samtools_report = open(filtered_reads_report).readlines()
assert '64962570 + 0 in total' in samtools_report[0] assert '64962570 + 0 in total' in samtools_report[0]
assert '64962570 + 0 mapped (100.00%:N/A)' in samtools_report[4] assert '64962570 + 0 mapped (100.00%:N/A)' in samtools_report[4]
...@@ -25,7 +25,7 @@ def test_map_qc_singleend(): ...@@ -25,7 +25,7 @@ def test_map_qc_singleend():
@pytest.mark.singleend @pytest.mark.singleend
def test_library_complexity_singleend(): def test_library_complexity_singleend():
library_complexity = test_output_path + 'ENCSR238SGC/ENCLB831RUI.pbc.qc' library_complexity = test_output_path + 'ENCLB831RUI/ENCLB831RUI.pbc.qc'
df_library_complexity = pd.read_csv(library_complexity, sep='\t') df_library_complexity = pd.read_csv(library_complexity, sep='\t')
assert df_library_complexity["NRF"].iloc[0] == 0.926192 assert df_library_complexity["NRF"].iloc[0] == 0.926192
assert df_library_complexity["PBC1"].iloc[0] == 0.926775 assert df_library_complexity["PBC1"].iloc[0] == 0.926775
...@@ -34,14 +34,14 @@ def test_library_complexity_singleend(): ...@@ -34,14 +34,14 @@ def test_library_complexity_singleend():
@pytest.mark.pairedend @pytest.mark.pairedend
def test_dedup_files_pairedend(): def test_dedup_files_pairedend():
assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC/ENCLB568IYX.dedup.bam')) assert os.path.exists(os.path.join(test_output_path, 'ENCLB568IYX/ENCLB568IYX.dedup.bam'))
assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC/ENCLB568IYX.dedup.bam.bai')) assert os.path.exists(os.path.join(test_output_path, 'ENCLB568IYX/ENCLB568IYX.dedup.bam.bai'))
assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC/ENCLB568IYX.dedup.qc')) assert os.path.exists(os.path.join(test_output_path, 'ENCLB568IYX/ENCLB568IYX.dedup.qc'))
@pytest.mark.pairedend @pytest.mark.pairedend
def test_map_qc_pairedend(): def test_map_qc_pairedend():
filtered_reads_report = test_output_path + 'ENCSR729LGA/ENCLB568IYX.dedup.flagstat.qc' filtered_reads_report = test_output_path + 'ENCLB568IYX/ENCLB568IYX.dedup.flagstat.qc'
samtools_report = open(filtered_reads_report).readlines() samtools_report = open(filtered_reads_report).readlines()
assert '47388510 + 0 in total' in samtools_report[0] assert '47388510 + 0 in total' in samtools_report[0]
assert '47388510 + 0 mapped (100.00%:N/A)' in samtools_report[4] assert '47388510 + 0 mapped (100.00%:N/A)' in samtools_report[4]
...@@ -49,7 +49,7 @@ def test_map_qc_pairedend(): ...@@ -49,7 +49,7 @@ def test_map_qc_pairedend():
@pytest.mark.pairedend @pytest.mark.pairedend
def test_library_complexity_pairedend(): def test_library_complexity_pairedend():
library_complexity = test_output_path + 'ENCSR729LGA/ENCLB568IYX.pbc.qc' library_complexity = test_output_path + 'ENCLB568IYX/ENCLB568IYX.pbc.qc'
df_library_complexity = pd.read_csv(library_complexity, sep='\t') df_library_complexity = pd.read_csv(library_complexity, sep='\t')
assert df_library_complexity["NRF"].iloc[0] == 0.947064 assert df_library_complexity["NRF"].iloc[0] == 0.947064
assert round(df_library_complexity["PBC1"].iloc[0],6) == 0.946723 assert round(df_library_complexity["PBC1"].iloc[0],6) == 0.946723
......
workflow/tests/test_map_reads.py
+ 4
− 4
View file @ 2f1c6283
...@@ -9,8 +9,8 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \ ...@@ -9,8 +9,8 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
@pytest.mark.singleend @pytest.mark.singleend
def test_map_reads_singleend(): def test_map_reads_singleend():
assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC/ENCLB831RUI.bam')) assert os.path.exists(os.path.join(test_output_path, 'ENCLB831RUI/ENCLB831RUI.bam'))
aligned_reads_report = test_output_path + 'ENCSR238SGC/ENCLB831RUI.flagstat.qc' aligned_reads_report = test_output_path + 'ENCLB831RUIENCLB831RUI/ENCLB831RUI.flagstat.qc'
samtools_report = open(aligned_reads_report).readlines() samtools_report = open(aligned_reads_report).readlines()
assert '80795025 + 0 in total' in samtools_report[0] assert '80795025 + 0 in total' in samtools_report[0]
assert '80050072 + 0 mapped (99.08% : N/A)' in samtools_report[4] assert '80050072 + 0 mapped (99.08% : N/A)' in samtools_report[4]
...@@ -18,8 +18,8 @@ def test_map_reads_singleend(): ...@@ -18,8 +18,8 @@ def test_map_reads_singleend():
@pytest.mark.pairedend @pytest.mark.pairedend
def test_map_reads_pairedend(): def test_map_reads_pairedend():
assert os.path.exists(os.path.join(test_output_path, 'ENCSR729LGA/ENCLB678IDC.bam')) assert os.path.exists(os.path.join(test_output_path, 'ENCLB678IDC/ENCLB678IDC.bam'))
aligned_reads_report = test_output_path + 'ENCSR729LGA/ENCLB678IDC.flagstat.qc' aligned_reads_report = test_output_path + 'ENCLB678IDC/ENCLB678IDC.flagstat.qc'
samtools_report = open(aligned_reads_report).readlines() samtools_report = open(aligned_reads_report).readlines()
assert '72660890 + 0 in total' in samtools_report[0] assert '72660890 + 0 in total' in samtools_report[0]
assert '72053925 + 0 mapped (99.16% : N/A)' in samtools_report[4] assert '72053925 + 0 mapped (99.16% : N/A)' in samtools_report[4]
......
workflow/tests/test_trim_reads.py
+ 6
− 6
View file @ 2f1c6283
...@@ -12,8 +12,8 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \ ...@@ -12,8 +12,8 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
@pytest.mark.singleend @pytest.mark.singleend
def test_trim_reads_singleend(): def test_trim_reads_singleend():
raw_fastq = test_data_path + 'ENCSR238SGC/ENCFF833BLU.fastq.gz' raw_fastq = test_data_path + 'ENCLB144FDT/ENCFF833BLU.fastq.gz'
trimmed_fastq = test_output_path + 'ENCSR238SGC/ENCLB144FDT_R1_trimmed.fq.gz' trimmed_fastq = test_output_path + 'ENCLB144FDT/ENCLB144FDT_R1_trimmed.fq.gz'
assert os.path.getsize(raw_fastq) != os.path.getsize(trimmed_fastq) assert os.path.getsize(raw_fastq) != os.path.getsize(trimmed_fastq)
assert os.path.getsize(trimmed_fastq) == 2512853101 assert os.path.getsize(trimmed_fastq) == 2512853101
...@@ -21,14 +21,14 @@ def test_trim_reads_singleend(): ...@@ -21,14 +21,14 @@ def test_trim_reads_singleend():
@pytest.mark.singleend @pytest.mark.singleend
def test_trim_report_singleend(): def test_trim_report_singleend():
trimmed_fastq_report = test_output_path + \ trimmed_fastq_report = test_output_path + \
'ENCSR238SGC/ENCLB144FDT_R1.fastq.gz_trimming_report.txt' 'ENCLB144FDT/ENCLB144FDT_R1.fastq.gz_trimming_report.txt'
assert 'Trimming mode: single-end' in open(trimmed_fastq_report).readlines()[4] assert 'Trimming mode: single-end' in open(trimmed_fastq_report).readlines()[4]
@pytest.mark.pairedend @pytest.mark.pairedend
def test_trim_reads_pairedend(): def test_trim_reads_pairedend():
raw_fastq = test_data_path + 'ENCSR729LGA/ENCFF582IOZ.fastq.gz' raw_fastq = test_data_path + 'ENCLB637LZP/ENCFF582IOZ.fastq.gz'
trimmed_fastq = test_output_path + 'ENCSR729LGA/ENCLB637LZP_R2_val_2.fq.gz' trimmed_fastq = test_output_path + 'ENCLB637LZP/ENCLB637LZP_R2_val_2.fq.gz'
assert os.path.getsize(raw_fastq) != os.path.getsize(trimmed_fastq) assert os.path.getsize(raw_fastq) != os.path.getsize(trimmed_fastq)
assert os.path.getsize(trimmed_fastq) == 2229312710 assert os.path.getsize(trimmed_fastq) == 2229312710
...@@ -36,5 +36,5 @@ def test_trim_reads_pairedend(): ...@@ -36,5 +36,5 @@ def test_trim_reads_pairedend():
@pytest.mark.pairedend @pytest.mark.pairedend
def test_trim_report_pairedend(): def test_trim_report_pairedend():
trimmed_fastq_report = test_output_path + \ trimmed_fastq_report = test_output_path + \
'ENCSR729LGA/ENCLB637LZP_R2.fastq.gz_trimming_report.txt' 'ENCLB637LZP/ENCLB637LZP_R2.fastq.gz_trimming_report.txt'
assert 'Trimming mode: paired-end' in open(trimmed_fastq_report).readlines()[4] assert 'Trimming mode: paired-end' in open(trimmed_fastq_report).readlines()[4]
workflow/tests/test_xcor.py
+ 4
− 4
View file @ 2f1c6283
...@@ -10,12 +10,12 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \ ...@@ -10,12 +10,12 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
@pytest.mark.singleend @pytest.mark.singleend
def test_cross_plot_singleend(): def test_cross_plot_singleend():
assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC/ENCLB144FDT.cc.plot.pdf')) assert os.path.exists(os.path.join(test_output_path, 'ENCLB144FDT/ENCLB144FDT.cc.plot.pdf'))
@pytest.mark.singleend @pytest.mark.singleend
def test_cross_qc_singleend(): def test_cross_qc_singleend():
qc_file = os.path.join(test_output_path,"ENCSR238SGC/ENCLB144FDT.cc.qc") qc_file = os.path.join(test_output_path,"ENCLB144FDT/ENCLB144FDT.cc.qc")
df_xcor = pd.read_csv(qc_file, sep="\t", header=None) df_xcor = pd.read_csv(qc_file, sep="\t", header=None)
assert df_xcor[2].iloc[0] == '190,200,210' assert df_xcor[2].iloc[0] == '190,200,210'
assert df_xcor[8].iloc[0] == 1.025906 assert df_xcor[8].iloc[0] == 1.025906
...@@ -24,12 +24,12 @@ def test_cross_qc_singleend(): ...@@ -24,12 +24,12 @@ def test_cross_qc_singleend():
@pytest.mark.pairedend @pytest.mark.pairedend
def test_cross_qc_pairedend(): def test_cross_qc_pairedend():
assert os.path.exists(os.path.join(test_output_path, 'ENCSR729LGA/ENCLB568IYX.cc.plot.pdf')) assert os.path.exists(os.path.join(test_output_path, 'ENCLB568IYX/ENCLB568IYX.cc.plot.pdf'))
@pytest.mark.pairedend @pytest.mark.pairedend
def test_cross_plot_pairedend(): def test_cross_plot_pairedend():
qc_file = os.path.join(test_output_path,"ENCSR729LGA/ENCLB568IYX.cc.qc") qc_file = os.path.join(test_output_path,"ENCLB568IYX/ENCLB568IYX.cc.qc")
df_xcor = pd.read_csv(qc_file, sep="\t", header=None) df_xcor = pd.read_csv(qc_file, sep="\t", header=None)
assert df_xcor[2].iloc[0] == '220,430,475' assert df_xcor[2].iloc[0] == '220,430,475'
assert round(df_xcor[8].iloc[0],6) == 1.060018 assert round(df_xcor[8].iloc[0],6) == 1.060018
......
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