prevent R mutations from being over written

theiagen · May 10, 2024 · 431be18 · 431be18
1 parent f63cd30
commit 431be18
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/tbp_parser/LIMS.py b/tbp_parser/LIMS.py
@@ -318,8 +318,8 @@ def apply_lims_rules(self, gene_dictionary, DF_LIMS, max_mdl_resistance, antimic
           self.logger.debug("LIMS:There are no mutations for this gene ({}) associated with this drug ({})".format(gene, antimicrobial_name))
           DF_LIMS[gene_code] = "No mutations detected"
 
-        if DF_LIMS[gene_code][0] == "No sequence":
-          self.logger.debug("LIMS:This gene has insufficient coverage; changing antimicrobial code")
+        if DF_LIMS[gene_code][0] == "No sequence" and max_mdl_resistance[0] != "R":
+          self.logger.debug("LIMS:This gene has insufficient coverage and the max resistance isn't R; changing antimicrobial code")
           DF_LIMS[antimicrobial_code] = "Pending Retest"
 
         if "Insufficient Coverage" in mdl_interpretations and max_mdl_resistance[0] in ["WT", "S", "Insufficient Coverage"]: