in src/main/python/vcf_annovar_annotation.py [0:0]
def variantScore(transcript,consequence_type,region,variant_type,dna,cdna,pro):
score1,score2 = 99,50
scores1 = {
'nonsense':0,
'nonstop':0,
'missense':1,
'in_frame':1,
'frameshift':2,
'start_codon':3,
'stop_codon':3,
'splice_site':4,
'miRNA':4,
'silent':5,
'synonymous':5,
'3-UTR':6,
'5-UTR':6,
'intron':7,
'flank':8,
'noncoding':9,
}
scores2 = {
'protein_coding':0,
'novel_protein_coding':1,
'nonsense_mediated_decay':2,
'nonstop_decay':3,
'processed_transcript':4,
'retained_intron':5,
'antisense':6,
'pseudogene':7,
'processed_pseudogene':8,
'translated_pseudogene':9,
'transcribed_pseudogene':10,
'unprocessed_pseudogene':11,
'polymorphic_pseudogene':12,
'unitary_pseudogene':13,
'non_coding':14,
'lincRNA':15,
'sense_intronic':16,
'sense_overlapping':17,
'macro_lncRNA':18,
'miRNA':19,
'piRNA':20,
'rRNA':21,
'siRNA':22,
'snRNA':23,
'snoRNA':24,
'tRNA':25,
'vaultRNA':26,
'unclassified_processed_transcript':27
}
if variant_type == 'nonsense':
score1 = 0
elif variant_type == 'nonstop':
score1 = 0
elif variant_type == 'start_codon_loss':
score1 = 0
elif variant_type == 'missense':
score1 = 1
elif variant_type == 'in_frame_insertion' or variant_type == 'in_frame_deletion':
score1 = 1
elif variant_type == 'frame_shift_insertion' or variant_type == 'frame_shift_deletion':
score1 = 2
elif variant_type == 'splice_site':
score1 = 4
elif variant_type == 'silent' or variant_type == 'synonymous':
score1 = 5
elif variant_type == '3-UTR' or variant_type =='5-UTR':
score1 = 6
elif variant_type == 'intron':
score1 = 7
elif variant_type == 'non-coding':
score1 = 9
if consequence_type in scores2:
score2 = scores2[consequence_type]
return score1,score2