def test_parse_callers_all(cyvcf2_variant, category):
# GIVEN all callers called a cancer variant
variant = cyvcf2_variant
variant.INFO['set'] = 'Intersection'
# WHEN parsing callers
parsed_callers = parse_callers(variant, category=category)
# THEN all callers should be in the dict
legal_callers = set(caller['id'] for caller in CALLERS[category])
assert legal_callers == set(parsed_callers.keys())
def test_parse_callers_all(cyvcf2_variant, category):
# GIVEN all callers called a cancer variant
variant = cyvcf2_variant
variant.INFO["set"] = "Intersection"
# WHEN parsing callers
parsed_callers = parse_callers(variant, category=category)
# THEN all callers should be in the dict
legal_callers = set(caller["id"] for caller in CALLERS[category])
assert legal_callers == set(parsed_callers.keys())
def test_parse_callers(one_vep104_annotated_variant):
variant = one_vep104_annotated_variant
assert variant.INFO["FOUND_IN"] == "deepvariant"
# WHEN parsing the caller info
callers = parse_callers(variant, category="snv")
# THEN the deep variant caller should be found, but not GATK
assert callers["deepvariant"] == "Pass"
assert callers["gatk"] == None
def test_parse_callers_intersection(cyvcf2_variant):
variant = cyvcf2_variant
# GIVEN information that all callers agree on Pass
variant.INFO['set'] = 'Intersection'
# WHEN parsing the information
callers = parse_callers(variant)
#THEN all callers should be passed
assert callers['gatk'] == 'Pass'
assert callers['freebayes'] == 'Pass'
assert callers['samtools'] == 'Pass'
def test_parse_callers_only_one(cyvcf2_variant):
variant = cyvcf2_variant
# GIVEN information about the variant callers
variant.INFO['set'] = 'gatk'
# WHEN parsing the information
callers = parse_callers(variant)
#THEN the correct callers should be passed
assert callers['gatk'] == 'Pass'
assert callers['freebayes'] == None
assert callers['samtools'] == None
def test_parse_callers(cyvcf2_variant):
variant = cyvcf2_variant
# GIVEN information that gatk and freebayes have passed
variant.INFO['set'] = 'gatk-freebayes'
# WHEN parsing the information
callers = parse_callers(variant)
#THEN the correct callers should be passed
assert callers['gatk'] == 'Pass'
assert callers['freebayes'] == 'Pass'
assert callers['samtools'] == None
def test_parse_callers_only_one(cyvcf2_variant):
variant = cyvcf2_variant
# GIVEN information about the variant callers
variant.INFO['set'] = 'gatk'
# WHEN parsing the information
callers = parse_callers(variant)
#THEN the correct callers should be passed
assert callers['gatk'] == 'Pass'
assert callers['freebayes'] == None
assert callers['samtools'] == None
def test_parse_callers_filtered_all(cyvcf2_variant):
variant = cyvcf2_variant
# GIVEN information that all callers agree on filtered
variant.INFO['set'] = 'FilteredInAll'
# WHEN parsing the information
callers = parse_callers(variant)
#THEN all callers should be filtered
assert callers['gatk'] == 'Filtered'
assert callers['freebayes'] == 'Filtered'
assert callers['samtools'] == 'Filtered'
def test_parse_callers(cyvcf2_variant):
variant = cyvcf2_variant
# GIVEN information that gatk and freebayes have passed
variant.INFO['set'] = 'gatk-freebayes'
# WHEN parsing the information
callers = parse_callers(variant)
#THEN the correct callers should be passed
assert callers['gatk'] == 'Pass'
assert callers['freebayes'] == 'Pass'
assert callers['samtools'] == None
def test_parse_callers_intersection(cyvcf2_variant):
variant = cyvcf2_variant
# GIVEN information that all callers agree on Pass
variant.INFO['set'] = 'Intersection'
# WHEN parsing the information
callers = parse_callers(variant)
#THEN all callers should be passed
assert callers['gatk'] == 'Pass'
assert callers['freebayes'] == 'Pass'
assert callers['samtools'] == 'Pass'
def test_parse_callers_complex(cyvcf2_variant):
variant = cyvcf2_variant
# GIVEN information about the variant callers
variant.INFO['set'] = 'gatk-filterInsamtools-freebayes'
# WHEN parsing the information
callers = parse_callers(variant)
#THEN the correct output should be returned
assert callers['gatk'] == 'Pass'
assert callers['freebayes'] == 'Pass'
assert callers['samtools'] == 'Filtered'
def test_parse_callers_filtered_all(cyvcf2_variant):
variant = cyvcf2_variant
# GIVEN information that all callers agree on filtered
variant.INFO['set'] = 'FilteredInAll'
# WHEN parsing the information
callers = parse_callers(variant)
#THEN all callers should be filtered
assert callers['gatk'] == 'Filtered'
assert callers['freebayes'] == 'Filtered'
assert callers['samtools'] == 'Filtered'
def test_parse_callers_complex(cyvcf2_variant):
variant = cyvcf2_variant
# GIVEN information about the variant callers
variant.INFO['set'] = 'gatk-filterInsamtools-freebayes'
# WHEN parsing the information
callers = parse_callers(variant)
#THEN the correct output should be returned
assert callers['gatk'] == 'Pass'
assert callers['freebayes'] == 'Pass'
assert callers['samtools'] == 'Filtered'
def test_parse_callers(cyvcf2_variant):
variant = cyvcf2_variant
# GIVEN information that gatk and freebayes have passed
variant.INFO["set"] = "gatk-freebayes"
# WHEN parsing the information
callers = parse_callers(variant)
# THEN the correct callers should be passed
assert callers["gatk"] == "Pass"
assert callers["freebayes"] == "Pass"
assert callers["samtools"] == None
def test_parse_callers_filtered_all(cyvcf2_variant):
variant = cyvcf2_variant
# GIVEN information that all callers agree on filtered
variant.INFO["set"] = "FilteredInAll"
# WHEN parsing the information
callers = parse_callers(variant)
# THEN all callers should be filtered
assert callers["gatk"] == "Filtered"
assert callers["freebayes"] == "Filtered"
assert callers["samtools"] == "Filtered"
def test_parse_callers_intersection(cyvcf2_variant):
variant = cyvcf2_variant
# GIVEN information that all callers agree on Pass
variant.INFO["set"] = "Intersection"
# WHEN parsing the information
callers = parse_callers(variant)
# THEN all callers should be passed
assert callers["gatk"] == "Pass"
assert callers["freebayes"] == "Pass"
assert callers["samtools"] == "Pass"
def test_parse_callers_complex(cyvcf2_variant):
variant = cyvcf2_variant
# GIVEN information about the variant callers
variant.INFO["set"] = "gatk-filterInsamtools-freebayes"
# WHEN parsing the information
callers = parse_callers(variant)
# THEN the correct output should be returned
assert callers["gatk"] == "Pass"
assert callers["freebayes"] == "Pass"
assert callers["samtools"] == "Filtered"
def test_parse_callers_only_one(cyvcf2_variant):
variant = cyvcf2_variant
# GIVEN information about the variant callers
variant.INFO["set"] = "gatk"
# WHEN parsing the information
callers = parse_callers(variant)
# THEN the correct callers should be passed
assert callers["gatk"] == "Pass"
assert callers["freebayes"] == None
assert callers["samtools"] == None
def test_parse_sv_callers_intersection(cyvcf2_variant):
variant = cyvcf2_variant
# GIVEN information that all callers agree on filtered
variant.INFO["set"] = "Intersection"
# WHEN parsing the information
callers = parse_callers(variant, category="sv")
# THEN all callers should be filtered
assert callers["cnvnator"] == "Pass"
assert callers["delly"] == "Pass"
assert callers["tiddit"] == "Pass"
assert callers["manta"] == "Pass"
def test_parse_sv_callers_filterin_tiddit(cyvcf2_variant):
variant = cyvcf2_variant
# GIVEN information that all callers agree on filtered
variant.INFO['set'] = 'manta-filterIntiddit'
# WHEN parsing the information
callers = parse_callers(variant, category='sv')
#THEN all callers should be filtered
assert callers['cnvnator'] == None
assert callers['delly'] == None
assert callers['tiddit'] == 'Filtered'
assert callers['manta'] == 'Pass'
def test_parse_sv_callers_intersection(cyvcf2_variant):
variant = cyvcf2_variant
variant.var_type = 'sv'
# GIVEN information that all callers agree on filtered
variant.INFO['set'] = 'Intersection'
# WHEN parsing the information
callers = parse_callers(variant)
#THEN all callers should be filtered
assert callers['cnvnator'] == 'Pass'
assert callers['delly'] == 'Pass'
assert callers['tiddit'] == 'Pass'
assert callers['manta'] == 'Pass'
