Skip to content
Snippets Groups Projects
Commit 7bddefc4 authored by Venkat Malladi's avatar Venkat Malladi
Browse files

Add in paired end test data.

parent cf982549
Branches
Tags
No related merge requests found
......@@ -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]
......
......@@ -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
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment