Commit a0a02958 authored by Jeremy Mathews's avatar Jeremy Mathews
Browse files

Update cross correlation and related tests

parent 1cd03ed1
Pipeline #4845 passed with stages
in 819 minutes and 23 seconds
......@@ -57,6 +57,7 @@ single_end_diff:
- master
script:
- nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' --astrocyte false -resume
- pytest -m singleend
- pytest -m singlediff
artifacts:
expire_in: 2 days
......@@ -67,6 +68,7 @@ paired_end_diff:
stage: multiple
script:
- nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_PE.txt" --genome 'GRCh38' --pairedEnd true --astrocyte false -resume
- pytest -m pairedend
- pytest -m paireddiff
artifacts:
expire_in: 2 days
......
......@@ -103,7 +103,7 @@ def xcor(tag, paired):
uncompressed_tag_filename = tag_basename
# Subsample tagAlign file
number_reads = 15000000
number_reads = 20000000
subsampled_tag_filename = \
tag_basename + ".%d.tagAlign.gz" % (number_reads/1000000)
......
......@@ -26,7 +26,7 @@ def test_peaks_xls_singleend():
@pytest.mark.singleend
def test_peaks_bed_singleend():
peak_file = test_output_path + 'ENCSR238SGC/1/' + 'ENCLB144FDT.narrowPeak'
assert utils.count_lines(peak_file) == 199317
assert utils.count_lines(peak_file) == 226738
@pytest.mark.pairedend
......@@ -47,4 +47,4 @@ def test_peaks_xls_pairedend():
@pytest.mark.pairedend
def test_peaks_bed_pairedend():
peak_file = test_output_path + 'ENCSR729LGA/2/' + 'ENCLB568IYX.narrowPeak'
assert utils.count_lines(peak_file) == 113821
assert utils.count_lines(peak_file) == 112631
......@@ -17,9 +17,9 @@ def test_cross_plot_singleend():
def test_cross_qc_singleend():
qc_file = os.path.join(test_output_path,"ENCLB144FDT/ENCLB144FDT.cc.qc")
df_xcor = pd.read_csv(qc_file, sep="\t", header=None)
assert df_xcor[2].iloc[0] == '220,240,255'
assert df_xcor[8].iloc[0] == 1.024935
assert round(df_xcor[9].iloc[0], 6) == 0.697252
assert df_xcor[2].iloc[0] == '185,195,205'
assert df_xcor[8].iloc[0] == 1.02454
assert df_xcor[9].iloc[0] == 0.8098014
@pytest.mark.pairedend
......@@ -31,6 +31,6 @@ def test_cross_qc_pairedend():
def test_cross_plot_pairedend():
qc_file = os.path.join(test_output_path,"ENCLB568IYX/ENCLB568IYX.cc.qc")
df_xcor = pd.read_csv(qc_file, sep="\t", header=None)
assert df_xcor[2].iloc[0] == '220,420,450'
assert round(df_xcor[8].iloc[0],6) == 1.058694
assert df_xcor[9].iloc[0] == 3.004596
assert df_xcor[2].iloc[0] == '215,225,455'
assert round(df_xcor[8].iloc[0],6) == 1.056201
assert df_xcor[9].iloc[0] == 3.599357
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