Fix bug: snps-within-gene using location

Genome3d · Jun 3, 2022 · 94e857b · 94e857b
1 parent 1b6f849
commit 94e857b
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/codes3d/codes3d.py b/codes3d/codes3d.py
@@ -747,7 +747,7 @@ def log_settings(args, logger):
     if args.gene_input:
         logger.write(f'--gene-input:\t{", ".join(args.gene_input)}')
     if args.snps_within_gene:
-        logger.write(f'--snps-within-gebe:\t{args.snps_within_gene}')
+        logger.write(f'--snps-within-gene:\t{args.snps_within_gene}')
     logger.write('\n')
 
 

diff --git a/codes3d/genes.py b/codes3d/genes.py
@@ -207,7 +207,7 @@ def get_gene_by_id(
 def get_gene_by_position(df, db):
     gene_df = []
     omitted_genes = []
-    sql = '''SELECT * FROM genes where chrom = '{}' and start= {} and "end" = {};'''
+    sql = '''SELECT * FROM genes where chrom = '{}' and start >= {} and "end" <= {};'''
     with db.connect() as con:
         for idx, row in df.iterrows():
             try: