Merge pull request #1365 from pavanvidem/pytest-bamPEFragmentSize

Pytest bam pe fragment size

pydeeptools/deeptools/test/test_bamPEFragmentSize.py

@@ -0,0 +1,45 @@
+import deeptools.bamPEFragmentSize
+from matplotlib.testing.compare import compare_images
+import os.path
+import filecmp
+from os import unlink
+from tempfile import NamedTemporaryFile
+
+ROOT = os.path.dirname(os.path.abspath(__file__)) + "/test_data"
+
+
+def test_bamPEFragmentSize_histogram():
+    """
+    Test histogram plot for bamPEFragmentSize
+    """
+    outfile = '/tmp/test_histogram.png'
+    args = "--bamfiles {}/bowtie2_test1.bam --samplesLabel bowtie2_test1.bam --plotFileFormat png --plotTitle Test-Plot --histogram {}".format(ROOT, outfile).split()
+    deeptools.bamPEFragmentSize.main(args)
+
+    res = compare_images(ROOT + '/bamPEFragmentSize_histogram_result1.png', outfile, 10)
+    assert res is None, res
+    unlink(outfile)
+
+def test_bamPEFragmentSize_fr_sizes():
+    """
+    Test fragment length information for bamPEFragmentSize
+    """
+    out_lengths = '/tmp/test_raw_frag_lengths.txt'
+    out_metrics = '/tmp/test_metrics_table.txt'
+    args = "--bamfiles {}/bowtie2_test1.bam --outRawFragmentLengths {} --table {}".format(ROOT, out_lengths, out_metrics).split()
+    deeptools.bamPEFragmentSize.main(args)
+
+    l = open(out_lengths, 'r')
+    l_resp = l.readlines()
+    l.close()
+    l_expected = ['241\t1', '242\t1', '251\t1']
+    matches = [expected for expected in l_expected if any(expected in resp for resp in l_resp)]
+    assert matches == l_expected
+
+    m = open(out_metrics, 'r')
+    m_resp = m.readlines()[1]
+    m.close()
+    m_expected = '3\t241.0\t241.5\t244.66666666666666\t242.0\t246.5\t251.0\t4.496912521077347\t1.0\t241.2\t241.4\t241.6\t241.8\t243.8\t245.6\t247.4\t249.2\t250.82\t3\t251.0\t251.0\t251.0\t251.0\t251.0\t251.0\t0.0\t0.0\t251.0\t251.0\t251.0\t251.0\t251.0\t251.0\t251.0\t251.0\t251.0\n'
+    assert m_expected in f"{m_resp}"
+    unlink(out_lengths)
+    unlink(out_metrics)