From d5884c4b083448826f5125538466b204f5100ab9 Mon Sep 17 00:00:00 2001 From: Thyago L Calvo Date: Thu, 10 Aug 2023 17:56:09 -0700 Subject: [PATCH] Update base_editing_guide_designs.py Fixed variant_summary.txt column name --- base_editing_guide_designs.py | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/base_editing_guide_designs.py b/base_editing_guide_designs.py index b30504b..5e644d9 100644 --- a/base_editing_guide_designs.py +++ b/base_editing_guide_designs.py @@ -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) @@ -451,8 +451,8 @@ def parse_variant_df(variant_df): 'ClinicalSignificance', 'PhenotypeList', 'ClinVar_SNP_Position', - 'ReferenceAllele', - 'AlternateAllele', + 'ReferenceAlleleVCF', + 'AlternateAlleleVCF', 'ReviewStatus']] return parsed_variant_df @@ -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 @@ -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 @@ -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', @@ -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