def validate(variant):
# check each values of variant
# genomic_ref
if variant.genomic_ref.strip() != '':
# check if starting with chr or nc_
if 'chr' in variant.genomic_ref.lower():
# check for numeric values after 'chr'
if not variant.genomic_ref[3:].isdigit():
return False
elif 'nc_' in variant.genomic_ref.lower():
# check for numeric values after 'nc_'
try:
float(variant.genomic_ref[3:])
except:
return False
else:
return False
# position
if variant.position.strip() != '':
# simple check if position is numeric
if not check_value(variant.position):
return False
# position_intron
if variant.position_intron.strip() != '':
# if position_intron has a value then position must have a value too.
if variant.position != '':
if not check_intron_value(variant.position_intron):
return False
else:
return False
# range_lower
if variant.range_lower.strip() != '':
# if there is a value in the range_lower then position must be empty
if variant.position.strip() == '':
if not check_value(variant.range_lower):
return False
else:
return False
# range_lower_intron
if variant.range_lower_intron.strip() != '':
# if range_lower_intron has a value then range_lower must have a value too.
if variant.range_lower.strip() != '':
if not check_intron_value(variant.range_lower_intron):
return False
else:
return False
# range_upper
if variant.range_upper.strip() != '':
# if range_upper has a value then range_lower must have a value to
if variant.range_lower.strip() != '':
if not check_value(variant.range_upper):
return False
else:
return False
# range_upper_intron
if variant.range_upper_intron.strip() != '':
# if range_upper_intron has a value then range_upper must hava a value too
if variant.range_upper.strip() != '':
if not check_intron_value(variant.range_upper_intron.strip()):
return False
else:
return False
operator_is_repeat = False
# operator
if variant.operator.strip() != '':
if variant.operator not in ValidValues.operators:
# if operator contains a '>'
if '>' in variant.operator:
# check if operator is a sub
if (variant.operator[0].lower() not in ValidValues.nucleotides):
return False
if (variant.operator[1] != '>'):
return False
if (variant.operator[2].lower() not in ValidValues.nucleotides):
return False
else:
# contains only nucleotides for repeat
if variant.operator[0].lower() in ValidValues.nucleotides:
i = 1 # check the 1st value move to next one
operator_is_repeat = True
while i < len(variant.operator):
if variant.operator[i].lower() in ValidValues.nucleotides:
i += 1
else:
return False
else:
# get the repeater range value
if not get_repeater_value(variant.operator):
return False
# operator value
if operator_is_repeat: # if operator is a repeat then we check the repeat range
if variant.operator_value:
if not get_repeater_value(variant.operator_value):
return False
# if it survived the checks then return true
return True
def validate(variant):
# Please not that since protein nomenclature is different to genomic/cDNA structure the values are
# stored differently in the VariantName Class.
# Since the protein positions and ranges contain the amino acid and numeric value for the index
# of that amino acid the variant position, range_lower and range_upper will store the amino acids
# while the intron fields will store the index.
# position: amino acid
if variant.position.strip() != '':
if variant.position not in ('?', '='):
if not variant.position.lower() in ValidValues.amino_acids:
if not variant.position.lower(
) in ValidValues.amino_acids_single:
return False
else:
return True
# position: index of the amino acid
if variant.position_intron.strip() != '':
# if position has a value then intron should too
if variant.position.strip() != '':
if not check_numeric_value(variant.position_intron):
return False
else:
return False
# range_lower: amino acid
if variant.range_lower.strip() != '':
if variant.position.strip() == '':
if not variant.range_lower.lower() in ValidValues.amino_acids:
return False
else:
return False
# range_lower: index of the amino acid
if variant.range_lower_intron.strip() != '':
if variant.range_lower.strip() != '':
if not check_numeric_value(variant.range_lower_intron):
return False
else:
return False
# range_upper: amino acid
if variant.range_upper.strip() != '':
if variant.range_lower.strip() != '':
if not variant.range_upper.lower() in ValidValues.amino_acids:
return False
else:
return False
# range_upper: index of the amino acid
if variant.range_upper_intron.strip() != '':
if variant.range_upper.strip() != '':
if not check_numeric_value(variant.range_upper_intron):
return False
else:
return False
# Operator
if variant.operator.strip() != '':
# check for repeating range
if not variant.operator[0] != '(' or not variant.operator[0] != '[':
if not get_repeater_value(variant.operator):
return False
# check for indels --> 'delins' and insertions --> 'ins'
elif variant.operator.lower() not in ValidValues.protein_operators:
# check for amino acids
if not variant.operator.lower() in ValidValues.amino_acids:
if not variant.operator.lower(
) in ValidValues.amino_acids_single:
return False
else:
return False
# Operator Value: should only contain amino acids for indel and insertion
# operators.
if variant.operator_value.strip() != '':
# frameshifts
if variant.operator_value[0:2] == 'fs':
if len(variant.operator_value) > 2:
if variant.operator_value[2].lower() in ('*', 'x'):
# check for '];['
if '];[' in variant.operator_value[3:]:
p = variant.operator_value.index('];[')
if variant.operator_value[3:p] != '':
if not variant.operator_value[3:p].isdigit():
return False
else:
if not variant.operator_value[3:].isdigit():
return False
else:
return False
else:
# ignore if operator begins with ']' or ')'
if ']' not in variant.operator_value and ')' not in variant.operator_value:
# operator value can not be empty if the operator is an indel or insertion
if variant.operator.lower(
) not in ValidValues.protein_operators:
# The length of operator string should be divisble by 3 since the amino acid
# codes should only be 3 chars long.
if not len(variant.operator_value) % 3 != 0:
return False
else:
# need to check each amino acid if valid
amino_acids = split(variant.operator_value.lower(), 3)
for amino_acid in amino_acids:
item_found = False
if amino_acid in ValidValues.amino_acids:
item_found = True
# if amino acid not found
if not item_found:
return False
return True
def validate(variant):
# Please not that since protein nomenclature is different to genomic/cDNA structure the values are
# stored differently in the VariantName Class.
# Since the protein positions and ranges contain the amino acid and numeric value for the index
# of that amino acid the variant position, range_lower and range_upper will store the amino acids
# while the intron fields will store the index.
# position: amino acid
if variant.position.strip() != '':
if variant.position not in ('?', '='):
if not variant.position.lower() in ValidValues.amino_acids:
if not variant.position.lower() in ValidValues.amino_acids_single:
return False
else:
return True
# position: index of the amino acid
if variant.position_intron.strip() != '':
# if position has a value then intron should too
if variant.position.strip() != '':
if not check_numeric_value(variant.position_intron):
return False
else:
return False
# range_lower: amino acid
if variant.range_lower.strip() != '':
if variant.position.strip() == '':
if not variant.range_lower.lower() in ValidValues.amino_acids:
return False
else:
return False
# range_lower: index of the amino acid
if variant.range_lower_intron.strip() != '':
if variant.range_lower.strip() != '':
if not check_numeric_value(variant.range_lower_intron):
return False
else:
return False
# range_upper: amino acid
if variant.range_upper.strip() != '':
if variant.range_lower.strip() != '':
if not variant.range_upper.lower() in ValidValues.amino_acids:
return False
else:
return False
# range_upper: index of the amino acid
if variant.range_upper_intron.strip() != '':
if variant.range_upper.strip() != '':
if not check_numeric_value(variant.range_upper_intron):
return False
else:
return False
# Operator
if variant.operator.strip() != '':
# check for repeating range
if not variant.operator[0] != '(' or not variant.operator[0] != '[':
if not get_repeater_value(variant.operator):
return False
# check for indels --> 'delins' and insertions --> 'ins'
elif variant.operator.lower() not in ValidValues.protein_operators:
# check for amino acids
if not variant.operator.lower() in ValidValues.amino_acids:
if not variant.operator.lower() in ValidValues.amino_acids_single:
return False
else:
return False
# Operator Value: should only contain amino acids for indel and insertion
# operators.
if variant.operator_value.strip() != '':
# frameshifts
if variant.operator_value[0:2] == 'fs':
if len(variant.operator_value) > 2:
if variant.operator_value[2].lower() in ('*', 'x'):
# check for '];['
if '];[' in variant.operator_value[3:]:
p = variant.operator_value.index('];[')
if variant.operator_value[3:p] != '':
if not variant.operator_value[3:p].isdigit():
return False
else:
if not variant.operator_value[3:].isdigit():
return False
else:
return False
else:
# ignore if operator begins with ']' or ')'
if ']' not in variant.operator_value and ')' not in variant.operator_value:
# operator value can not be empty if the operator is an indel or insertion
if variant.operator.lower() not in ValidValues.protein_operators:
# The length of operator string should be divisble by 3 since the amino acid
# codes should only be 3 chars long.
if not len(variant.operator_value) % 3 != 0:
return False
else:
# need to check each amino acid if valid
amino_acids = split(variant.operator_value.lower(), 3)
for amino_acid in amino_acids:
item_found = False
if amino_acid in ValidValues.amino_acids:
item_found = True
# if amino acid not found
if not item_found:
return False
return True