class TestReportPy(unittest.TestCase):
""" test the Report class
"""
def setUp(self):
""" define a family and variant, and start the Allosomal class
"""
# generate a test family
child_gender = "F"
mom_aff = "1"
dad_aff = "1"
self.trio = self.create_family(child_gender, mom_aff, dad_aff)
# generate a test variant
child_var = self.create_snv(child_gender, "0/1")
mom_var = self.create_snv("F", "0/0")
dad_var = self.create_snv("M", "0/0")
var = TrioGenotypes(child_var)
var.add_mother_variant(mom_var)
var.add_father_variant(dad_var)
self.variants = [var]
self.report = Report(None, None, None, None)
self.report.family = self.trio
# self.report.tags_dict = tags
def create_snv(self, gender, genotype):
""" create a default variant
"""
chrom = "X"
pos = "15000000"
snp_id = "."
ref = "A"
alt = "G"
qual = "50"
filt = "PASS"
# set up a SNV object, since SNV inherits VcfInfo
var = SNV(chrom, pos, snp_id, ref, alt, filt)
info = "HGNC=TEST;CQ=missense_variant;random_tag;EUR_AF=0.0005"
format_keys = "GT:DP"
sample_values = genotype + ":50"
var.vcf_line = [chrom, pos, snp_id, ref, alt, qual, filt, info, format_keys, sample_values]
var.add_info(info)
var.add_format(format_keys, sample_values)
var.set_gender(gender)
var.set_genotype()
return var
def create_family(self, child_gender, mom_aff, dad_aff):
""" create a default family, with optional gender and parental statuses
"""
fam = Family("test")
fam.add_child("child", "child_vcf", "2", child_gender)
fam.add_mother("mother", "mother_vcf", mom_aff, "2")
fam.add_father("father", "father_vcf", dad_aff, "1")
fam.set_child()
return fam
def test__get_provenance(self):
""" check that _get_provenance() works correctly
"""
prov = ["checksum", "sample.calls.date.vcf.gz", "2014-01-01"]
member = "proband"
self.assertEqual(self.report._get_provenance(prov, member), \
["##UberVCF_proband_Id=sample\n", \
"##UberVCF_proband_Checksum=checksum\n", \
"##UberVCF_proband_Basename=sample.calls.date.vcf.gz\n", \
"##UberVCF_proband_Date=2014-01-01\n"])
def test__get_vcf_export_path(self):
""" check that _get_vcf_export_path() works correctly
"""
# use a folder to place the VCFG file in, which means we join the
# proband ID to get a full path
self.report.export_vcf = os.getcwd()
self.assertEqual(self.report._get_vcf_export_path(), os.path.join(os.getcwd(), "child.vcf.gz"))
# define an un-uable directory, to raise an error
self.report.export_vcf = os.getcwd() + "asjhfgasjhfg"
self.assertRaises(ValueError, self.report._get_vcf_export_path)
# define a specific path for a VCF file, which is returned directly
self.report.export_vcf = os.path.join(os.getcwd(), "sample_id.vcf.gz")
self.assertEqual(self.report._get_vcf_export_path(), self.report.export_vcf)
def test__make_vcf_header(self):
""" check that _make_vcf_header() works correctly
"""
# define the intial header lines
header = ["####fileformat=VCFv4.1\n",
"##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\n",
"#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\sample_id\n"]
# define the VCF provenances
provenance = [("checksum", "proband.calls.date.vcf.gz", "2014-01-01"),
("checksum", "mother.calls.date.vcf.gz", "2014-01-02"),
("checksum", "father.calls.date.vcf.gz", "2014-01-03")]
processed_header = ["####fileformat=VCFv4.1\n",
"##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\n",
'##INFO=<ID=ClinicalFilterType,Number=.,Type=String,Description="The type of clinical filter that passed this variant.">\n',
'##INFO=<ID=ClinicalFilterGeneInheritance,Number=.,Type=String,Description="The inheritance mode (Monoallelic, Biallelic etc) under which the variant was found.">\n',
'##INFO=<ID=ClinicalFilterReportableHGNC,Number=.,Type=String,Description="The HGNC symbol which the variant was identified as being reportable for.">\n',
'##FORMAT=<ID=INHERITANCE_GENOTYPE,Number=.,Type=String,Description="The 012 coded genotypes for a trio (child, mother, father).">\n',
'##FORMAT=<ID=INHERITANCE,Number=.,Type=String,Description="The inheritance of the variant in the trio (biparental, paternal, maternal, deNovo).">\n',
"##ClinicalFilterRunDate={0}\n".format(datetime.date.today()),
"##ClinicalFilterVersion=XXX\n",
"##ClinicalFilterHistory=single_variant,compound_het\n",
"##UberVCF_proband_Id=proband\n",
"##UberVCF_proband_Checksum=checksum\n",
"##UberVCF_proband_Basename=proband.calls.date.vcf.gz\n",
"##UberVCF_proband_Date=2014-01-01\n",
"##UberVCF_maternal_Id=mother\n",
"##UberVCF_maternal_Checksum=checksum\n",
"##UberVCF_maternal_Basename=mother.calls.date.vcf.gz\n",
"##UberVCF_maternal_Date=2014-01-02\n",
"##UberVCF_paternal_Id=father\n",
"##UberVCF_paternal_Checksum=checksum\n",
"##UberVCF_paternal_Basename=father.calls.date.vcf.gz\n",
"##UberVCF_paternal_Date=2014-01-03\n",
"#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\sample_id\n"]
# check that the standard function returns the expected value. Note that
# I haven't checked the output if self.known_genes_date is not None, nor
# have I checked if the _clinicalFilterVersion is available
self.assertEqual(self.report._make_vcf_header(header, provenance),
processed_header)
def test__get_parental_inheritance(self):
""" check that _get_parental_inheritance() works correctly
"""
var = self.variants[0]
# check for the default genotypes
self.assertEqual(self.report._get_parental_inheritance(var), "deNovo")
# check when only the mother is non-ref
var.mother.genotype = 1
self.assertEqual(self.report._get_parental_inheritance(var), "maternal")
# check when both parents are non-ref
var.father.genotype = 1
self.assertEqual(self.report._get_parental_inheritance(var), "biparental")
# check when only the father is non-ref
var.mother.genotype = 0
self.assertEqual(self.report._get_parental_inheritance(var), "paternal")
# check when the proband lacks parental information
self.report.family.father = None
self.report.family.mother = None
self.assertEqual(self.report._get_parental_inheritance(var), "unknown")
def test__get_vcf_lines(self):
""" check that _get_vcf_lines() works correctly
"""
# define the intial header lines
header = ["####fileformat=VCFv4.1\n",
"##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\n",
"#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\sample_id\n"]
# define the VCF provenances
provenance = [("checksum", "proband.calls.date.vcf.gz", "2014-01-01"),
("checksum", "mother.calls.date.vcf.gz", "2014-01-02"),
("checksum", "father.calls.date.vcf.gz", "2014-01-03")]
# define what the header will become
vcf_lines = ["####fileformat=VCFv4.1\n",
"##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\n",
'##INFO=<ID=ClinicalFilterType,Number=.,Type=String,Description="The type of clinical filter that passed this variant.">\n',
'##INFO=<ID=ClinicalFilterGeneInheritance,Number=.,Type=String,Description="The inheritance mode (Monoallelic, Biallelic etc) under which the variant was found.">\n',
'##INFO=<ID=ClinicalFilterReportableHGNC,Number=.,Type=String,Description="The HGNC symbol which the variant was identified as being reportable for.">\n',
'##FORMAT=<ID=INHERITANCE_GENOTYPE,Number=.,Type=String,Description="The 012 coded genotypes for a trio (child, mother, father).">\n',
'##FORMAT=<ID=INHERITANCE,Number=.,Type=String,Description="The inheritance of the variant in the trio (biparental, paternal, maternal, deNovo).">\n',
"##ClinicalFilterRunDate={0}\n".format(datetime.date.today()),
"##ClinicalFilterVersion=XXX\n",
"##ClinicalFilterHistory=single_variant,compound_het\n",
"##UberVCF_proband_Id=proband\n",
"##UberVCF_proband_Checksum=checksum\n",
"##UberVCF_proband_Basename=proband.calls.date.vcf.gz\n",
"##UberVCF_proband_Date=2014-01-01\n",
"##UberVCF_maternal_Id=mother\n",
"##UberVCF_maternal_Checksum=checksum\n",
"##UberVCF_maternal_Basename=mother.calls.date.vcf.gz\n",
"##UberVCF_maternal_Date=2014-01-02\n",
"##UberVCF_paternal_Id=father\n",
"##UberVCF_paternal_Checksum=checksum\n",
"##UberVCF_paternal_Basename=father.calls.date.vcf.gz\n",
"##UberVCF_paternal_Date=2014-01-03\n",
"#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\sample_id\n"]
# define what the default variant vcf line will become
line = ["X\t15000000\t.\tA\tG\t50\tPASS\tHGNC=TEST;CQ=missense_variant;random_tag;EUR_AF=0.0005;ClinicalFilterGeneInheritance=Monoallelic;ClinicalFilterType=single_variant;ClinicalFilterReportableHGNC=TEST\tGT:DP:INHERITANCE:INHERITANCE_GENOTYPE\t0/1:50:deNovo:1,0,0\n"]
# check that a list of one variant produces the correct VCF output. Note
# that we haven't checked against CNVs, which can change the
# INHERITANCE_GENOTYPE flag, nor have we tested a larger list of variants
var = (self.variants[0], ["single_variant"], ["Monoallelic"], ["TEST"])
self.assertEqual(self.report._get_vcf_lines([var], header, provenance), vcf_lines + line)
def test__get_output_line(self):
""" check that _get_output_line() works correctly
"""
var = (self.variants[0], ["single_variant"], ["Monoallelic"], ["TEST"])
dad_aff = "0"
mom_aff = "1"
alt_id = "test_id"
# check the output for the default variant
expected = "child\ttest_id\tF\tX\t15000000\tTEST\tNA\tNA\tmissense_variant\tA/G\t0.0005\tMonoallelic\t1/0/0\t1\t0\tsingle_variant\tNA\tNA\n"
self.assertEqual(self.report._get_output_line(var, dad_aff, mom_aff, alt_id), expected)
# introduce additional info for the output line parsing, check the line
# that is returned is expected
var[0].child.info["PolyPhen"] = "probably_damaging(0.99)"
var[0].child.info["SIFT"] = "deleterious(0)"
var[0].child.info["ENST"] = "ENST00X"
expected = "child\ttest_id\tF\tX\t15000000\tTEST\tNA\tENST00X\tmissense_variant,PolyPhen=probably_damaging(0.99),SIFT=deleterious(0)\tA/G\t0.0005\tMonoallelic\t1/0/0\t1\t0\tsingle_variant\tNA\tNA\n"
self.assertEqual(self.report._get_output_line(var, dad_aff, mom_aff, alt_id), expected)
class TestReportPy(unittest.TestCase):
""" test the Report class
"""
def setUp(self):
""" define a family and variant, and start the Allosomal class
"""
# generate a test family
child_gender = "F"
mom_aff = "1"
dad_aff = "1"
self.trio = self.create_family(child_gender, mom_aff, dad_aff)
# generate a test variant
child_var = self.create_snv(child_gender, "0/1")
mom_var = self.create_snv("F", "0/0")
dad_var = self.create_snv("M", "0/0")
var = TrioGenotypes(child_var)
var.add_mother_variant(mom_var)
var.add_father_variant(dad_var)
self.variants = [var]
self.report = Report(None, None, None, None)
self.report.family = self.trio
# self.report.tags_dict = tags
def create_snv(self, gender, genotype):
""" create a default variant
"""
chrom = "X"
pos = "15000000"
snp_id = "."
ref = "A"
alt = "G"
qual = "50"
filt = "PASS"
# set up a SNV object, since SNV inherits VcfInfo
var = SNV(chrom, pos, snp_id, ref, alt, filt)
info = "HGNC=TEST;CQ=missense_variant;random_tag;EUR_AF=0.0005"
format_keys = "GT:DP"
sample_values = genotype + ":50"
var.vcf_line = [
chrom, pos, snp_id, ref, alt, qual, filt, info, format_keys,
sample_values
]
var.add_info(info)
var.add_format(format_keys, sample_values)
var.set_gender(gender)
var.set_genotype()
return var
def create_family(self, child_gender, mom_aff, dad_aff):
""" create a default family, with optional gender and parental statuses
"""
fam = Family("test")
fam.add_child("child", "child_vcf", "2", child_gender)
fam.add_mother("mother", "mother_vcf", mom_aff, "2")
fam.add_father("father", "father_vcf", dad_aff, "1")
fam.set_child()
return fam
def test__get_provenance(self):
""" check that _get_provenance() works correctly
"""
prov = ["checksum", "sample.calls.date.vcf.gz", "2014-01-01"]
member = "proband"
self.assertEqual(self.report._get_provenance(prov, member), \
["##UberVCF_proband_Id=sample\n", \
"##UberVCF_proband_Checksum=checksum\n", \
"##UberVCF_proband_Basename=sample.calls.date.vcf.gz\n", \
"##UberVCF_proband_Date=2014-01-01\n"])
def test__get_vcf_export_path(self):
""" check that _get_vcf_export_path() works correctly
"""
# use a folder to place the VCFG file in, which means we join the
# proband ID to get a full path
self.report.export_vcf = os.getcwd()
self.assertEqual(self.report._get_vcf_export_path(),
os.path.join(os.getcwd(), "child.vcf.gz"))
# define an un-uable directory, to raise an error
self.report.export_vcf = os.getcwd() + "asjhfgasjhfg"
self.assertRaises(ValueError, self.report._get_vcf_export_path)
# define a specific path for a VCF file, which is returned directly
self.report.export_vcf = os.path.join(os.getcwd(), "sample_id.vcf.gz")
self.assertEqual(self.report._get_vcf_export_path(),
self.report.export_vcf)
def test__make_vcf_header(self):
""" check that _make_vcf_header() works correctly
"""
# define the intial header lines
header = [
"####fileformat=VCFv4.1\n",
"##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\n",
"#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\sample_id\n"
]
# define the VCF provenances
provenance = [("checksum", "proband.calls.date.vcf.gz", "2014-01-01"),
("checksum", "mother.calls.date.vcf.gz", "2014-01-02"),
("checksum", "father.calls.date.vcf.gz", "2014-01-03")]
processed_header = [
"####fileformat=VCFv4.1\n",
"##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\n",
'##INFO=<ID=ClinicalFilterType,Number=.,Type=String,Description="The type of clinical filter that passed this variant.">\n',
'##INFO=<ID=ClinicalFilterGeneInheritance,Number=.,Type=String,Description="The inheritance mode (Monoallelic, Biallelic etc) under which the variant was found.">\n',
'##FORMAT=<ID=INHERITANCE_GENOTYPE,Number=.,Type=String,Description="The 012 coded genotypes for a trio (child, mother, father).">\n',
'##FORMAT=<ID=INHERITANCE,Number=.,Type=String,Description="The inheritance of the variant in the trio (biparental, paternal, maternal, deNovo).">\n',
"##ClinicalFilterRunDate={0}\n".format(
datetime.date.today()), "##ClinicalFilterVersion=XXX\n",
"##ClinicalFilterHistory=single_variant,compound_het\n",
"##UberVCF_proband_Id=proband\n",
"##UberVCF_proband_Checksum=checksum\n",
"##UberVCF_proband_Basename=proband.calls.date.vcf.gz\n",
"##UberVCF_proband_Date=2014-01-01\n",
"##UberVCF_maternal_Id=mother\n",
"##UberVCF_maternal_Checksum=checksum\n",
"##UberVCF_maternal_Basename=mother.calls.date.vcf.gz\n",
"##UberVCF_maternal_Date=2014-01-02\n",
"##UberVCF_paternal_Id=father\n",
"##UberVCF_paternal_Checksum=checksum\n",
"##UberVCF_paternal_Basename=father.calls.date.vcf.gz\n",
"##UberVCF_paternal_Date=2014-01-03\n",
"#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\sample_id\n"
]
# check that the standard function returns the expected value. Note that
# I haven't checked the output if self.known_genes_date is not None, nor
# have I checked if the _clinicalFilterVersion is available
self.assertEqual(self.report._make_vcf_header(header, provenance),
processed_header)
def test__get_parental_inheritance(self):
""" check that _get_parental_inheritance() works correctly
"""
var = self.variants[0]
# check for the default genotypes
self.assertEqual(self.report._get_parental_inheritance(var), "deNovo")
# check when only the mother is non-ref
var.mother.genotype = 1
self.assertEqual(self.report._get_parental_inheritance(var),
"maternal")
# check when both parents are non-ref
var.father.genotype = 1
self.assertEqual(self.report._get_parental_inheritance(var),
"biparental")
# check when only the father is non-ref
var.mother.genotype = 0
self.assertEqual(self.report._get_parental_inheritance(var),
"paternal")
# check when the proband lacks parental information
self.report.family.father = None
self.report.family.mother = None
self.assertEqual(self.report._get_parental_inheritance(var), "unknown")
def test__get_vcf_lines(self):
""" check that _get_vcf_lines() works correctly
"""
# define the intial header lines
header = [
"####fileformat=VCFv4.1\n",
"##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\n",
"#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\sample_id\n"
]
# define the VCF provenances
provenance = [("checksum", "proband.calls.date.vcf.gz", "2014-01-01"),
("checksum", "mother.calls.date.vcf.gz", "2014-01-02"),
("checksum", "father.calls.date.vcf.gz", "2014-01-03")]
# define what the header will become
vcf_lines = [
"####fileformat=VCFv4.1\n",
"##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">\n",
'##INFO=<ID=ClinicalFilterType,Number=.,Type=String,Description="The type of clinical filter that passed this variant.">\n',
'##INFO=<ID=ClinicalFilterGeneInheritance,Number=.,Type=String,Description="The inheritance mode (Monoallelic, Biallelic etc) under which the variant was found.">\n',
'##FORMAT=<ID=INHERITANCE_GENOTYPE,Number=.,Type=String,Description="The 012 coded genotypes for a trio (child, mother, father).">\n',
'##FORMAT=<ID=INHERITANCE,Number=.,Type=String,Description="The inheritance of the variant in the trio (biparental, paternal, maternal, deNovo).">\n',
"##ClinicalFilterRunDate={0}\n".format(
datetime.date.today()), "##ClinicalFilterVersion=XXX\n",
"##ClinicalFilterHistory=single_variant,compound_het\n",
"##UberVCF_proband_Id=proband\n",
"##UberVCF_proband_Checksum=checksum\n",
"##UberVCF_proband_Basename=proband.calls.date.vcf.gz\n",
"##UberVCF_proband_Date=2014-01-01\n",
"##UberVCF_maternal_Id=mother\n",
"##UberVCF_maternal_Checksum=checksum\n",
"##UberVCF_maternal_Basename=mother.calls.date.vcf.gz\n",
"##UberVCF_maternal_Date=2014-01-02\n",
"##UberVCF_paternal_Id=father\n",
"##UberVCF_paternal_Checksum=checksum\n",
"##UberVCF_paternal_Basename=father.calls.date.vcf.gz\n",
"##UberVCF_paternal_Date=2014-01-03\n",
"#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\sample_id\n"
]
# define what the default variant vcf line will become
line = [
"X\t15000000\t.\tA\tG\t50\tPASS\tHGNC=TEST;CQ=missense_variant;random_tag;EUR_AF=0.0005;ClinicalFilterGeneInheritance=Monoallelic;ClinicalFilterType=single_variant\tGT:DP:INHERITANCE:INHERITANCE_GENOTYPE\t0/1:50:deNovo:1,0,0\n"
]
# check that a list of one variant produces the correct VCF output. Note
# that we haven't checked against CNVs, which can change the
# INHERITANCE_GENOTYPE flag, nor have we tested a larger list of variants
var = (self.variants[0], "single_variant", "Monoallelic")
self.assertEqual(self.report._get_vcf_lines([var], header, provenance),
vcf_lines + line)
def test__get_output_line(self):
""" check that _get_output_line() works correctly
"""
var = (self.variants[0], "single_variant", "Monoallelic")
dad_aff = "0"
mom_aff = "1"
alt_id = "test_id"
# check the output for the default variant
expected = "child\ttest_id\tF\tX\t15000000\tTEST\tNA\tNA\tmissense_variant\tA/G\t0.0005\tMonoallelic\t1/0/0\t1\t0\tsingle_variant\n"
self.assertEqual(
self.report._get_output_line(var, dad_aff, mom_aff, alt_id),
expected)
# introduce additional info for the output line parsing, check the line
# that is returned is expected
var[0].child.info["PolyPhen"] = "probably_damaging(0.99)"
var[0].child.info["SIFT"] = "deleterious(0)"
var[0].child.info["ENST"] = "ENST00X"
expected = "child\ttest_id\tF\tX\t15000000\tTEST\tNA\tENST00X\tmissense_variant,PolyPhen=probably_damaging(0.99),SIFT=deleterious(0)\tA/G\t0.0005\tMonoallelic\t1/0/0\t1\t0\tsingle_variant\n"
self.assertEqual(
self.report._get_output_line(var, dad_aff, mom_aff, alt_id),
expected)
