added unit tests for check ped parsing

src/test/python/clinicalfilter/test_load_ped.py

@@ -0,0 +1,132 @@
+""" unit testing of loading ped files
+"""
+
+import unittest
+import tempfile
+
+from clinicalfilter.ped import load_ped_file, load_families, Person, Family
+
+class TestLoadPed(unittest.TestCase):
+    """
+    """
+
+    def setUp(self):
+        """ define and write a temporary ped file
+        """
+
+        self.tempfile = tempfile.NamedTemporaryFile(mode="w")
+        self.path = self.tempfile.name
+
+        self.tempfile.write("fam_ID   proband   dad   mom   F  2  /path/to/proband_vcf.gz\n")
+        self.tempfile.write("fam_ID   dad       0     0     M  1  /path/to/dad_vcf.gz\n")
+        self.tempfile.write("fam_ID   mom       0     0     F  1  /path/to/mom_vcf.gz\n")
+        self.tempfile.flush()
+
+    def test_load_ped_file_single_family(self):
+        """ check that we correctly parse a ped file with a single trio
+        """
+
+        # load all the components from the file
+        mothers, fathers, children, affected, sex, vcfs = load_ped_file(self.path)
+
+        # check that they all match
+        self.assertEqual(mothers, {'mom': '0', 'proband': 'mom', 'dad': '0'})
+        self.assertEqual(fathers, {'mom': '0', 'proband': 'dad', 'dad': '0'})
+        self.assertEqual(children, {'proband': 'fam_ID'})
+        self.assertEqual(affected, {'mom': '1', 'proband': '2', 'dad': '1'})
+        self.assertEqual(sex, {'mom': 'F', 'proband': 'F', 'dad': 'M'})
+        self.assertEqual(vcfs, {'mom': '/path/to/mom_vcf.gz', \
+            'proband': '/path/to/proband_vcf.gz', \
+            'dad': '/path/to/dad_vcf.gz'})
+
+    def test_load_ped_file_multiple_sibs(self):
+        """ check that we correctly parse a ped file with multiple siblings
+        """
+
+        # add an extra sibling
+        self.tempfile.write("fam_ID  sib   dad  mom  F  2  /path/to/sib_vcf.gz\n")
+        self.tempfile.flush()
+
+        # load all the components from the file
+        mothers, fathers, children, affected, sex, vcfs = load_ped_file(self.path)
+
+        # check that they all match
+        self.assertEqual(mothers, {'mom': '0', 'proband': 'mom', 'dad': '0', 'sib': 'mom'})
+        self.assertEqual(fathers, {'mom': '0', 'proband': 'dad', 'dad': '0', 'sib': 'dad'})
+        self.assertEqual(children, {'proband': 'fam_ID', "sib": "fam_ID"})
+        self.assertEqual(affected, {'mom': '1', 'proband': '2', 'dad': '1', 'sib': '2'})
+        self.assertEqual(sex, {'mom': 'F', 'proband': 'F', 'dad': 'M', 'sib': 'F'})
+        self.assertEqual(vcfs, {'mom': '/path/to/mom_vcf.gz',
+            'proband': '/path/to/proband_vcf.gz',
+            'dad': '/path/to/dad_vcf.gz',
+            'sib': '/path/to/sib_vcf.gz'})
+
+    def test_load_ped_file_multiple_families(self):
+        """ check that we correctly parse a ped file with multiple families
+        """
+
+        # add an extra family, with multiple sibs
+        self.tempfile.write("fam_ID2  proband2  dad2  mom2  F  2  /path/to/proband2_vcf.gz\n")
+        self.tempfile.write("fam_ID2  dad2      0     0     M  1  /path/to/dad2_vcf.gz\n")
+        self.tempfile.write("fam_ID2  mom2      0     0     F  1  /path/to/mom2_vcf.gz\n")
+        self.tempfile.write("fam_ID2  sib       dad2  mom2  F  2  /path/to/sib_vcf.gz\n")
+        self.tempfile.flush()
+
+        # load all the components from the file
+        mothers, fathers, children, affected, sex, vcfs = load_ped_file(self.path)
+
+        # check that they all match
+        self.assertEqual(mothers, {'mom': '0', 'proband': 'mom', 'dad': '0',
+            'mom2': '0', 'proband2': 'mom2', 'dad2': '0', 'sib': 'mom2'})
+        self.assertEqual(fathers, {'mom': '0', 'proband': 'dad', 'dad': '0',
+            'mom2': '0', 'proband2': 'dad2', 'dad2': '0', 'sib': 'dad2'})
+        self.assertEqual(children, {'proband': 'fam_ID',
+            "proband2": "fam_ID2", "sib": "fam_ID2"})
+        self.assertEqual(affected, {'mom': '1', 'proband': '2', 'dad': '1',
+            'mom2': '1', 'proband2': '2', 'dad2': '1', 'sib': '2'})
+        self.assertEqual(sex, {'mom': 'F', 'proband': 'F', 'dad': 'M',
+            'mom2': 'F', 'proband2': 'F', 'dad2': 'M', 'sib': 'F'})
+        self.assertEqual(vcfs, {'mom': '/path/to/mom_vcf.gz',
+            'proband': '/path/to/proband_vcf.gz',
+            'dad': '/path/to/dad_vcf.gz',
+            'proband2': '/path/to/proband2_vcf.gz',
+            'dad2': '/path/to/dad2_vcf.gz',
+            'mom2': '/path/to/mom2_vcf.gz',
+            'sib': '/path/to/sib_vcf.gz'})
+
+    def test_load_families(self):
+        """ check that load_families works correctly
+        """
+
+        # construct a temporary family that will have the same sample IDs etc
+        # as for the one loaded from the ped file.
+        family = Family("fam_ID")
+        family.add_child("proband", "/path/to/proband_vcf.gz", "2", "F")
+        family.add_mother("mom", "/path/to/mom_vcf.gz", "1", "F")
+        family.add_father("dad", "/path/to/dad_vcf.gz", "1", "M")
+
+        # load the ped file, and check that the load_families function returns
+        # the expected Family object
+        families = load_families(self.path)
+        self.assertEqual(families, {"fam_ID": family})
+
+        # add an extra family, with multiple sibs
+        self.tempfile.write("fam_ID2  proband2 dad2  mom2  F  2  /path/to/proband2_vcf.gz\n")
+        self.tempfile.write("fam_ID2  dad2     0     0     M  1  /path/to/dad2_vcf.gz\n")
+        self.tempfile.write("fam_ID2  mom2     0     0     F  1  /path/to/mom2_vcf.gz\n")
+        self.tempfile.write("fam_ID2  sib      dad2  mom2  F  2  /path/to/sib_vcf.gz\n")
+        self.tempfile.flush()
+
+        # construct a temporary family that will have the same sample IDs etc
+        # as for the one loaded from the ped file.
+        fam2 = Family("fam_ID2")
+        fam2.add_child("proband2", "/path/to/proband2_vcf.gz", "2", "F")
+        fam2.add_child("sib", "/path/to/sib_vcf.gz", "2", "F")
+        fam2.add_mother("mom2", "/path/to/mom2_vcf.gz", "1", "F")
+        fam2.add_father("dad2", "/path/to/dad2_vcf.gz", "1", "M")
+
+        # load the ped file, and check that the load_families function returns
+        # the expected Families objects
+        families = load_families(self.path)
+        self.assertEqual(set(families.values()), set([family, fam2]))
+