#389 alleles checker added

py_src/ChunkQC.py

@@ -2,7 +2,9 @@
 import pandas as pd
 from collections import defaultdict
 
-nomenclature_set = set(pd.read_csv('../patches/IGM_nomenclature_table.tsv', sep='\t')['IMGT/GENE-DB'])
+nomenclature_df = pd.read_csv('../patches/IGM_nomenclature_table.tsv', sep='\t')
+nomenclature_set = set(nomenclature_df['IMGT/GENE-DB'])
+alleles_dict = nomenclature_df.set_index('IMGT/GENE-DB')['Number of alleles'].to_dict()
 
 COMPLEX_COLUMNS = [
     "cdr3.alpha",
@@ -181,3 +183,17 @@ def gene_match_check(gene_name: str) -> bool:
         return gene_name in nomenclature_set
     return True
 
+
+def alleles_match_check(gene_name: str) -> bool:
+    if isinstance(gene_name, str):
+        gene = gene_name.split('*')[0]
+        if len(gene_name.split('*')) > 1:
+            allele = gene_name.split('*')[1]
+        else:
+            return True
+        if gene not in nomenclature_set:
+            return True
+        else:
+            return int(allele) <= alleles_dict[gene]
+    else:
+        return True

py_src/runBuidDatabase.py

@@ -5,7 +5,7 @@
 from termcolor import cprint
 
 
-from ChunkQC import ChunkQC, ALL_COLS, gene_match_check
+from ChunkQC import ChunkQC, ALL_COLS, gene_match_check, alleles_match_check
 from Cdr3Fixer import Cdr3Fixer
 from DefaultDBGenerator import generate_default_db
 from SlimDBGenerator import generate_slim_db
@@ -84,16 +84,22 @@
     master_table.to_pickle('../database/vdjdb_full.pkl', )
 
     mask_gene_list = []
+    mask_alleles_list = []
     for gene in ['alpha', 'beta']:
         mask_gene_list.append(master_table[f'v.{gene}'].apply(gene_match_check))
         mask_gene_list.append(master_table[f'j.{gene}'].apply(gene_match_check))
-    final_mask = mask_gene_list[0]
+        mask_alleles_list.append(master_table[f'v.{gene}'].apply(alleles_match_check))
+        mask_alleles_list.append(master_table[f'j.{gene}'].apply(alleles_match_check))
 
-    for mask in mask_gene_list[1:]:
+    final_mask = mask_gene_list[0]
+    final_mask_alleles = mask_alleles_list[0]
+    for mask, allele_mask in zip(mask_gene_list[1:], mask_alleles_list[1:]):
         final_mask = final_mask & mask
+        final_mask_alleles = final_mask_alleles & allele_mask
 
-    master_table.loc[final_mask].set_index('cdr3.alpha').to_csv('../database/vdjdb_full_gene_clear.txt', sep='\t')
+    master_table.loc[final_mask & final_mask_alleles].set_index('cdr3.alpha').to_csv('../database/vdjdb_full_gene_clear.txt', sep='\t')
     master_table.loc[~final_mask].set_index('cdr3.alpha').to_csv('../database/vdjdb_full_gene_broken.txt', sep='\t')
+    master_table.loc[~final_mask_alleles].set_index('cdr3.alpha').to_csv('../database/vdjdb_full_allele_broken.txt', sep='\t')
 
     cprint("Generating and writing default database", 'magenta')
     default_db = generate_default_db(master_table)