Commit 2e987ca1 authored by Spencer Barnes's avatar Spencer Barnes
Browse files

modify path in align reads pytest

parent f98fd03f
Pipeline #7431 failed with stages
in 98 minutes and 36 seconds
......@@ -14,22 +14,22 @@ def test_map_reads_singleend():
assert 'Mapping efficiency:\t42.9%\n' in samtools_report[8]
assert "Total number of C's analysed:\t145657914\n" in samtools_report[23]
assert os.path.exists(os.path.join(test_output_path, '/liver2/ENCFF000MCD_hsap_hepato_rep2_trimmed_bismark_bt2.bam'))
aligned_reads_report = test_output_path + '/liver2/ENCFF000MCD_hsap_hepato_rep2_trimmed_bismark_bt2_SE_report.txt'
assert os.path.exists(os.path.join(test_output_path, 'liver2/ENCFF000MCD_hsap_hepato_rep2_trimmed_bismark_bt2.bam'))
aligned_reads_report = test_output_path + 'liver2/ENCFF000MCD_hsap_hepato_rep2_trimmed_bismark_bt2_SE_report.txt'
samtools_report = open(aligned_reads_report).readlines()
assert 'Sequences analysed in total:\t36753283\n' in samtools_report[6]
assert 'Mapping efficiency:\t35.8%\n' in samtools_report[8]
assert "Total number of C's analysed:\t141487023\n" in samtools_report[23]
assert os.path.exists(os.path.join(test_output_path, '/lung1/ENCFF000MDS_hsap_lung_rrbs_rep1_trimmed_bismark_bt2.bam'))
aligned_reads_report = test_output_path + '/lung1/ENCFF000MDS_hsap_lung_rrbs_rep1_trimmed_bismark_bt2_SE_report.txt'
assert os.path.exists(os.path.join(test_output_path, 'lung1/ENCFF000MDS_hsap_lung_rrbs_rep1_trimmed_bismark_bt2.bam'))
aligned_reads_report = test_output_path + 'lung1/ENCFF000MDS_hsap_lung_rrbs_rep1_trimmed_bismark_bt2_SE_report.txt'
samtools_report = open(aligned_reads_report).readlines()
assert 'Sequences analysed in total:\t41727993\n' in samtools_report[6]
assert 'Mapping efficiency:\t15.3%\n' in samtools_report[8]
assert "Total number of C's analysed:\t69933546\n" in samtools_report[23]
assert os.path.exists(os.path.join(test_output_path, '/lung2/ENCFF000MDT_hsap__lung_rep2_trimmed_bismark_bt2.bam'))
aligned_reads_report = test_output_path + '/lung2/ENCFF000MDT_hsap__lung_rep2_trimmed_bismark_bt2_SE_report.txt'
assert os.path.exists(os.path.join(test_output_path, 'lung2/ENCFF000MDT_hsap__lung_rep2_trimmed_bismark_bt2.bam'))
aligned_reads_report = test_output_path + 'lung2/ENCFF000MDT_hsap__lung_rep2_trimmed_bismark_bt2_SE_report.txt'
samtools_report = open(aligned_reads_report).readlines()
assert 'Sequences analysed in total:\t37152735\n' in samtools_report[6]
assert 'Mapping efficiency:\t32.5%\n' in samtools_report[8]
......@@ -37,29 +37,29 @@ def test_map_reads_singleend():
@pytest.mark.pairedend
def test_map_reads_pairedend():
assert os.path.exists(os.path.join(test_output_path, '/heart1/heart_a_S2_R1_001_val_1_bismark_bt2_pe.bam'))
aligned_reads_report = test_output_path + '/heart1/heart_a_S2_R1_001_val_1_bismark_bt2_PE_report.txt'
assert os.path.exists(os.path.join(test_output_path, 'heart1/heart_a_S2_R1_001_val_1_bismark_bt2_pe.bam'))
aligned_reads_report = test_output_path + 'heart1/heart_a_S2_R1_001_val_1_bismark_bt2_PE_report.txt'
samtools_report = open(aligned_reads_report).readlines()
assert 'Sequence pairs analysed in total:\t18107045\n' in samtools_report[6]
assert 'Mapping efficiency:\t57.3%\n' in samtools_report[8]
assert "Total number of C's analysed:\t345193812\n" in samtools_report[23]
assert os.path.exists(os.path.join(test_output_path, '/heart2/heart_b_S4_R1_001_val_1_bismark_bt2_pe.bam'))
aligned_reads_report = test_output_path + '/heart2/heart_b_S4_R1_001_val_1_bismark_bt2_PE_report.txt'
assert os.path.exists(os.path.join(test_output_path, 'heart2/heart_b_S4_R1_001_val_1_bismark_bt2_pe.bam'))
aligned_reads_report = test_output_path + 'heart2/heart_b_S4_R1_001_val_1_bismark_bt2_PE_report.txt'
samtools_report = open(aligned_reads_report).readlines()
assert 'Sequence pairs analysed in total:\t12016511\n' in samtools_report[6]
assert 'Mapping efficiency:\t51.4%\n' in samtools_report[8]
assert "Total number of C's analysed:\t200311991\n" in samtools_report[23]
assert os.path.exists(os.path.join(test_output_path, '/liver1/liver_a_S4_R1_001_val_1_bismark_bt2_pe.bam'))
aligned_reads_report = test_output_path + '/liver1/liver_a_S4_R1_001_val_1_bismark_bt2_PE_report.txt'
assert os.path.exists(os.path.join(test_output_path, 'liver1/liver_a_S4_R1_001_val_1_bismark_bt2_pe.bam'))
aligned_reads_report = test_output_path + 'liver1/liver_a_S4_R1_001_val_1_bismark_bt2_PE_report.txt'
samtools_report = open(aligned_reads_report).readlines()
assert 'Sequence pairs analysed in total:\t16444589\n' in samtools_report[6]
assert 'Mapping efficiency:\t55.9%\n' in samtools_report[8]
assert "Total number of C's analysed:\t310540010\n" in samtools_report[23]
assert os.path.exists(os.path.join(test_output_path, '/liver2/Liver_b_S2_R1_001_val_1_bismark_bt2_pe.bam'))
aligned_reads_report = test_output_path + '/liver2/Liver_b_S2_R1_001_val_1_bismark_bt2_PE_report.txt'
assert os.path.exists(os.path.join(test_output_path, 'liver2/Liver_b_S2_R1_001_val_1_bismark_bt2_pe.bam'))
aligned_reads_report = test_output_path + 'liver2/Liver_b_S2_R1_001_val_1_bismark_bt2_PE_report.txt'
samtools_report = open(aligned_reads_report).readlines()
assert 'Sequence pairs analysed in total:\t8166172\n' in samtools_report[6]
assert 'Mapping efficiency:\t50.0%\n' in samtools_report[8]
......
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