Added pytest for ComputeMatrix along with associated test files

pydeeptools/deeptools/test/test_computeMatrix.py

@@ -0,0 +1,61 @@
+import deeptools.computeMatrix as cm
+
+import os.path
+from os import unlink
+
+ROOT = os.path.dirname(os.path.abspath(__file__)) + "/test_data/"
+REGIONS_IN1 = ROOT + "computeMatrix1.bed"
+REGIONS_IN2 = ROOT + "computeMatrix2.bed"
+BIGWIG_IN1 = ROOT + "bamCoverage_result4.bw"
+BIGWIG_IN2 = ROOT + "computeMatrix2.bw"
+OUT_ARCHIEVE1 = ROOT + "computeMatrix_result1.gz"
+OUT_ARCHIEVE2 = ROOT + "computeMatrix_result2.gz"
+OUT_ARCHIEVE3 = ROOT + "computeMatrix_result3.gz"
+
+def test_compute_matrix_with_reference_point_and_advance_options_1():
+    """
+    Test minimal command line args compute matrix with reference based
+    mode along with advance options of sorting using sum and average 
+    type bin as sum
+    """
+    outfile = '/tmp/computematrix_1.gz'
+    args = "reference-point --regionsFileName {} --scoreFileName {} -o {} -bs 10 --sortUsing sum --averageTypeBins sum -b 10 -a 10".format(REGIONS_IN1, BIGWIG_IN1, outfile).split()
+    cm.main(args)
+
+    archieve_file_size = os.path.getsize(OUT_ARCHIEVE1)
+    expected_file_size = os.path.getsize(outfile)
+    size_tolerance = 500
+    size_difference = abs(archieve_file_size - expected_file_size)
+    assert size_difference <= size_tolerance, "File size do not match"
+    unlink(outfile)
+
+def test_compute_matrix_with_reference_point_and_advance_options_2():
+    """
+    Test minimal command line args compute matrix with reference based mode 
+    with before and after region start length
+    """
+    outfile = '/tmp/computematrix_2.gz'
+    args = "reference-point --regionsFileName {} --scoreFileName {} -o {} -bs 10 -b 10 -a 10".format(REGIONS_IN2, BIGWIG_IN2, outfile).split()
+    cm.main(args)
+
+    archieve_file_size = os.path.getsize(OUT_ARCHIEVE2)
+    expected_file_size = os.path.getsize(outfile)
+    size_tolerance = 500
+    size_difference = abs(archieve_file_size - expected_file_size)
+    assert size_difference <= size_tolerance, "File size do not match"
+    unlink(outfile)
+
+def test_compute_matrix_with_scale_regions():
+    """
+    Test minimal command line args compute matrix with scale regions mode
+    """
+    outfile = '/tmp/computematrix_3.gz'
+    args = "scale-regions --regionsFileName {} --scoreFileName {} -o {}".format(REGIONS_IN2, BIGWIG_IN2, outfile).split()
+    cm.main(args)
+
+    archieve_file_size = os.path.getsize(OUT_ARCHIEVE3)
+    expected_file_size = os.path.getsize(outfile)
+    size_tolerance = 500
+    size_difference = abs(archieve_file_size - expected_file_size)
+    assert size_difference <= size_tolerance, "File size do not match"
+    unlink(outfile)

pydeeptools/deeptools/test/test_data/computeMatrix1.bed

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+phiX174	1000	1500	CG11023	0	+
+phiX174	150	1750	cda5	0	-
+phiX174	150	177	cda8	0	-
+phiX174	75	1500	cda9	0	+
+phiX174	101	175	C11023	0	+
+phiX174	125	150	ca5	0	-
+phiX174	450	1750	ca8	0	+
+phiX174	80	1500	cda9	0	+

pydeeptools/deeptools/test/test_data/computeMatrix2.bed

@@ -0,0 +1,6 @@
+ch1	100	150	CG11023	0	+
+ch2	150	175	cda5	0	-
+ch3	100	125	cda8	0	+
+ch1	75	125	C11023	0	+
+ch2	125	150	ca5	0	-
+ch3	75	100	ca8	0	+