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Update base_editing_guide_designs.py #5

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Update base_editing_guide_designs.py #5

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20 changes: 10 additions & 10 deletions base_editing_guide_designs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -439,7 +439,7 @@ def parse_variant_df(variant_df):
& (variant_df.Type == 'single nucleotide variant')
& (variant_df.Chromosome != 'MT')
& (variant_df.Chromosome != 'na')
& (variant_df.ReferenceAllele != 'na')]
& (variant_df.ReferenceAlleleVCF != 'na')]
parsed_variant_df = temp_variant_df.copy()
parsed_variant_df.index = range(0,len(parsed_variant_df))
parsed_variant_df.rename(columns = {'Start':'ClinVar_SNP_Position'}, inplace=True)
Expand All @@ -451,8 +451,8 @@ def parse_variant_df(variant_df):
'ClinicalSignificance',
'PhenotypeList',
'ClinVar_SNP_Position',
'ReferenceAllele',
'AlternateAllele',
'ReferenceAlleleVCF',
'AlternateAlleleVCF',
'ReviewStatus']]
return parsed_variant_df

Expand Down Expand Up @@ -548,7 +548,7 @@ def get_snps(edit_map, edit, sg_gen_pos, gene_strand, sgrna_strand, gene_variant
codon_pos_list, edit_gen_pos_list = get_genomic_pos_list(edit_indices, gene_strand, sgrna_strand, sg_gen_pos)
# Check if there is any overlap between codon_pos_list and all_snps
if any(i in codon_pos_list for i in all_snps):
clinvar_snps_df = gene_variant_df[gene_variant_df.ClinVar_SNP_Position.isin(codon_pos_list)].loc[:,['Name','ClinicalSignificance','ClinVar_SNP_Position','ReferenceAllele','AlternateAllele','ReviewStatus']]
clinvar_snps_df = gene_variant_df[gene_variant_df.ClinVar_SNP_Position.isin(codon_pos_list)].loc[:,['Name','ClinicalSignificance','ClinVar_SNP_Position','ReferenceAlleleVCF','AlternateAlleleVCF','ReviewStatus']]
for index,row in clinvar_snps_df.iterrows():
snp_aa, snp_aa_from, snp_aa_num, snp_aa_to = parse_snp_name(row.Name, aa_map)
# First check for nucleotide position
Expand All @@ -559,13 +559,13 @@ def get_snps(edit_map, edit, sg_gen_pos, gene_strand, sgrna_strand, gene_variant
same_nucleotide_pos = True
# If sgRNA is in the forward strand, C>T or A>G SNPs will be created
if ((gene_strand == 1) and (sgrna_strand == 'sense') or ((gene_strand == -1) and sgrna_strand == 'antisense')):
if row.AlternateAllele == edit_to:
if row.AlternateAlleleVCF == edit_to:
same_nucleotide_change = True
else:
same_nucleotide_change = False
# If sgRNA is in the reverse strand, G>A or T>C SNPs will be created
elif ((gene_strand == 1) and (sgrna_strand == 'antisense') or ((gene_strand == -1) and sgrna_strand == 'sense')):
if row.AlternateAllele == revcom(edit_to):
if row.AlternateAlleleVCF == revcom(edit_to):
same_nucleotide_change = True
else:
same_nucleotide_change = False
Expand Down Expand Up @@ -1095,8 +1095,8 @@ def read_args(args):
edit = args.edit
variant_file = args.variant_file
variant_df = pd.read_table(variant_file, dtype = {'#AlleleID':str, 'Name':str, 'ClinicalSignificance':str, 'Assembly':str,
'Chromosome':str,'Type':str,'Start':int,'ReferenceAllele':str,
'AlternateAllele':str,'ReviewStatus':str}, usecols = ['#AlleleID',
'Chromosome':str,'Type':str,'Start':int,'ReferenceAlleleVCF':str,
'AlternateAlleleVCF':str,'ReviewStatus':str}, usecols = ['#AlleleID',
'GeneSymbol',
'Name',
'ClinicalSignificance',
Expand All @@ -1105,8 +1105,8 @@ def read_args(args):
'Chromosome',
'Type',
'Start',
'ReferenceAllele',
'AlternateAllele',
'ReferenceAlleleVCF',
'AlternateAlleleVCF',
'ReviewStatus'])
parsed_variant_df = parse_variant_df(variant_df)
output_name = args.output_name
Expand Down