def add_leading_base(chr, pos, ref, alt, seq_provider):
pos = int(pos)
empty_ref = False
empty_alt = False
if utilities.isEmpty(ref):
ref = ""
empty_ref = True
if utilities.isEmpty(alt):
alt = ""
empty_alt = True
seq = seq_provider.get_seq(int(chr), pos - 1, 2)
seq_pos = 1
if empty_ref is True and empty_alt is True:
raise Exception("both ref and alt are empty")
elif empty_ref is True:
# If the ref is empty, get the base at the position and append it to ref and alt
leading_base = seq[seq_pos]
return (chr, str(pos), leading_base + ref, leading_base + alt)
elif empty_alt is True:
# If the alt is empty, get the base at the position just before where the deletion happens
# and append it to the ref and alt
leading_base = seq[seq_pos - 1]
return (chr, str(pos - 1), leading_base + ref, leading_base + alt)
else:
raise Exception("add leading base called but both ref and alt were provided!")
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 prepare_variant_for_removal_and_log(original_hgvs, normalized_hgvs, items,
bx_ids_for_variant, reason_for_discard,
variants_to_remove):
if reason_for_discard == "Incorrect Reference":
logging.warning("Ref incorrect using %s", normalized_hgvs)
logging.warning(
"Original variant representation of incorrect ref variant before add_leading_base: %s",
str(items))
elif reason_for_discard == "Variant ref and alt are the same":
logging.warning("Variant ref and alt are the same for variant %s",
normalized_hgvs)
logging.warning("Original variant representation: %s", str(items))
else:
logging.warning("Bad data for variant: %s", normalized_hgvs)
logging.warning("Original variant representation: %s", str(items))
for key in bx_ids_for_variant.keys():
reports = bx_ids_for_variant[key]
if utilities.isEmpty(reports):
continue
else:
prefix = "BX_ID_"
source = key[len(prefix):]
log_discarded_reports(source, reports, normalized_hgvs,
reason_for_discard)
variants_to_remove.append(original_hgvs)
return variants_to_remove
def seekPattern(self, id, textArray, seekFirstMatch = True):
method=self.base.getMethod(id)
matches=[]
for alg in method:
for pattern in alg:
for line in textArray:
found=re.compile(pattern, flags = re.IGNORECASE).search(line)
if(utilities.hasValue(found)):
matches.append(found.group())
# print(matches)
# print("next alg")
# print((seekFirstMatch and (utilities.isEmpty(matches))))
if(seekFirstMatch and (not utilities.isEmpty(matches))):
break
return matches
def getNumericAFValue(value):
if isEmpty(value):
return 0
else:
return float(value)