add pytest for correctGCBias

deeptools · Jan 22, 2025 · 3f2e806 · 3f2e806
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diff --git a/pydeeptools/deeptools/test/test_correctGCBias.py b/pydeeptools/deeptools/test/test_correctGCBias.py
@@ -0,0 +1,26 @@
+# from unittest import TestCase
+
+import deeptools.correctGCBias
+import deeptools.utilities
+import os.path
+from os import unlink
+import pysam
+
+ROOT = os.path.dirname(os.path.abspath(__file__)) + "/test_data/"
+
+
+def test_correctGCBias():
+    """
+    Test minimal command line args for correctGCBias
+    """
+    GCbiasFreq = ROOT + 'computeGCBias_result1.tabular'
+    BAM = ROOT + 'paired_chr2L.bam'
+    GENOME = ROOT + 'sequence.2bit'
+    outfile = '/tmp/test_correctbias.bam'
+    args = "--GCbiasFrequenciesFile {} --bamfile {} --genome {} --effectiveGenomeSize 10050 --correctedFile {}".format(GCbiasFreq, BAM, GENOME, outfile).split()
+    deeptools.correctGCBias.main(args)
+
+    alignment_count = pysam.AlignmentFile(outfile, "rb").count()
+    expected_count = 11630
+    assert abs(alignment_count - expected_count) < 50
+    unlink(outfile)