def append_exac_allele_frequencies(record, new_record=None, i=None):
if new_record is None:
for subpopulation in EXAC_SUBPOPULATIONS:
# calculate allele frequencies for each subpopulation
allele_count = record.INFO[("AC_" + subpopulation)]
allele_number = record.INFO[("AN_" + subpopulation)]
allele_frequency = "-"
if len(allele_count) > 0 and allele_number != 0:
allele_frequency = float(
allele_count[0]) / float(allele_number)
allele_frequency = str(
utilities.round_sigfigs(allele_frequency, 3))
record.INFO[("AF_" + subpopulation)] = allele_frequency
return record
else:
new_record.INFO['AF'] = record.INFO['AF'][i]
for subpopulation in EXAC_SUBPOPULATIONS:
allele_count = record.INFO[("AC_" + subpopulation)][i]
allele_number = record.INFO[("AN_" + subpopulation)]
allele_frequency = "-"
if allele_number != 0:
allele_frequency = float(allele_count) / float(allele_number)
allele_frequency = str(
utilities.round_sigfigs(allele_frequency, 3))
new_record.INFO[("AF_" + subpopulation)] = allele_frequency
return new_record
def determineGnomADAlleleFrequency(row):
if isEmpty(row['Allele_frequency_genome_GnomAD']) and isEmpty(row['Allele_frequency_exome_GnomAD']):
return EMPTY
else:
ac_genome = getNumericAFValue(row['Allele_count_genome_GnomAD'])
an_genome = getNumericAFValue(row['Allele_number_genome_GnomAD'])
ac_exome = getNumericAFValue(row['Allele_count_exome_GnomAD'])
an_exome = getNumericAFValue(row['Allele_number_exome_GnomAD'])
if (an_genome + an_exome) == 0:
return EMPTY
return round_sigfigs(((ac_genome + ac_exome) / (an_genome + an_exome)), 4)
def test_append_exac_allele_frequencies_rounds_to_three_sig_figs(self):
EXAC_VCF_FILENAME = os.path.join(os.path.dirname(__file__), 'test_files/ExAC_AF.vcf')
for record in vcf.Reader(open(EXAC_VCF_FILENAME, 'r')):
record = append_exac_allele_frequencies(record, new_record=None, i=None)
for subpopulation in EXAC_SUBPOPULATIONS:
val = record.INFO["AF_" + subpopulation]
try:
float_val = float(val)
self.assertEqual(float_val, round_sigfigs(float(val), 3))
except ValueError:
self.assertEqual(val, '-')
def test_append_exac_allele_frequencies_rounds_to_three_sig_figs(self):
EXAC_VCF_FILENAME = os.path.join(os.path.dirname(__file__),
'test_files/ExAC_AF.vcf')
for record in vcf.Reader(open(EXAC_VCF_FILENAME, 'r')):
record = append_exac_allele_frequencies(record,
new_record=None,
i=None)
for subpopulation in EXAC_SUBPOPULATIONS:
val = record.INFO["AF_" + subpopulation]
try:
float_val = float(val)
self.assertEqual(float_val, round_sigfigs(float(val), 3))
except ValueError:
self.assertEqual(val, '-')
def append_exac_allele_frequencies(record, new_record=None, i=None):
if new_record is None:
for subpopulation in EXAC_SUBPOPULATIONS:
# calculate allele frequencies for each subpopulation
allele_count = record.INFO[("AC_" + subpopulation)]
allele_number = record.INFO[("AN_" + subpopulation)]
allele_frequency = "-"
if len(allele_count) > 0 and allele_number != 0:
allele_frequency = float(allele_count[0]) / float(allele_number)
allele_frequency = str(utilities.round_sigfigs(allele_frequency, 3))
record.INFO[("AF_" + subpopulation)] = allele_frequency
return record
else:
new_record.INFO['AF'] = record.INFO['AF'][i]
for subpopulation in EXAC_SUBPOPULATIONS:
allele_count = record.INFO[("AC_" + subpopulation)][i]
allele_number = record.INFO[("AN_" + subpopulation)]
allele_frequency = "-"
if allele_number != 0:
allele_frequency = float(allele_count) / float(allele_number)
allele_frequency = str(utilities.round_sigfigs(allele_frequency, 3))
new_record.INFO[("AF_" + subpopulation)] = allele_frequency
return new_record
def selectMaxAlleleFrequency(newRow):
maxFreq = 0
maxFreqString = EMPTY
allele_frequency_fields = [
"EA_Allele_Frequency_ESP",
"AA_Allele_Frequency_ESP",
"Allele_Frequency_ESP",
"EUR_Allele_frequency_1000_Genomes",
"AFR_Allele_frequency_1000_Genomes",
"AMR_Allele_frequency_1000_Genomes",
"EAS_Allele_frequency_1000_Genomes",
"SAS_Allele_frequency_1000_Genomes",
"Allele_frequency_AFR_ExAC",
"Allele_frequency_AMR_ExAC",
"Allele_frequency_EAS_ExAC",
"Allele_frequency_FIN_ExAC",
"Allele_frequency_NFE_ExAC",
"Allele_frequency_OTH_ExAC",
"Allele_frequency_SAS_ExAC"
]
for field in allele_frequency_fields:
if newRow[field] != EMPTY and newRow[field] != None:
freqs = [float(i) for i in newRow[field].split(',')]
max_in_field = max(freqs)
if max_in_field > maxFreq:
source = determineSourceForMAF(field)
subpopulation = determineSubpopulationForMAF(field)
maxFreq = max_in_field
if "ExAC" in source:
# Ensure exac values maintain 3 sigfigs
maxFreqStringPrefix = str(utilities.round_sigfigs(float(max_in_field), 3))
maxFreqStringSuffix = " (%s from %s)" % (subpopulation, source)
maxFreqString = maxFreqStringPrefix + maxFreqStringSuffix
else:
maxFreqString = "%f (%s from %s)" % (max_in_field, subpopulation, source)
return(maxFreqString)
