Merge branch 'armfinder_nomenclature_update' into 'main'

Update nomenclature from amrfinder

See merge request !11

module/utils.py

@@ -137,32 +137,39 @@ def armfinder_to_table(data_resistance:pd.DataFrame) ->  pd.DataFrame:
                    'POINTX' : "!",
                    'BLASTX' : "*",
                    'PARTIALX' : "?",
-                   'PARTIAL_CONTIG_ENDX' : "?$", #The PARTIAL_CONTIG_ENDX method is only attributedd when the start or end position of the sequence being searched coincides exactly with the start or end of the contig.
+                   'PARTIAL_CONTIG_ENDX' : "_end_of_contig", #The PARTIAL_CONTIG_ENDX method is only attributedd when the start or end position of the sequence being searched coincides exactly with the start or end of the contig.
+                   'CTRL_CONTIG_END' : "_end_of_contig",
                    'INTERNAL_STOP' :  "#"}
+    
+    avoid_NTTB_prediction = ['PARTIAL_CONTIG_ENDX',
+                             'CTRL_CONTIG_END']
+
     data_resistance['Class'] = data_resistance['Class'].fillna ('NoClass')
     Class = data_resistance['Class'].value_counts().keys()
     Strains = data_resistance['Name'].value_counts().keys()
     table = pd.DataFrame('',index=Strains, columns=Class)
 
     for res in data_resistance.index :
-        gene = data_resistance['Gene symbol'][res] + dico_Method[data_resistance['Method'][res]]      
-        
-        if 'tox' in data_resistance['Gene symbol'][res] : 
-            if float(data_resistance['% Coverage of reference sequence'][res]) != 100.00 :
-                    if (data_resistance['Method'][res] == 'BLASTX') :
-                        gene = data_resistance['Gene symbol'][res] + "-NTTB?-"+str(round(100-float(data_resistance['% Coverage of reference sequence'][res])))+"%"              
-                    else :
-                        gene = data_resistance['Gene symbol'][res] + "-NTTB" + dico_Method[data_resistance['Method'][res]]
-
-        if is_contig_edge(data_resistance.iloc[res]) : # Used to find certain cases of interruption due to a contig end that AMRfinder is unable to find. 
-            gene = f"{data_resistance['Gene symbol'][res]}_end_of_contig"
-            
+        gene = data_resistance['Gene symbol'][res] + dico_Method[data_resistance['Method'][res]]
+        # Search for certain cases of interruption due to a contig end that AMRfinder is unable to find.    
+        if is_contig_edge(data_resistance.iloc[res]) : 
+            data_resistance['Method'][res] = "CTRL_CONTIG_END" 
+
+        if ('tox' in data_resistance['Gene symbol'][res]) and \
+           (float(data_resistance['% Coverage of reference sequence'][res]) != 100.00) and \
+           (data_resistance['Method'][res] not in avoid_NTTB_prediction) :
+                gene = data_resistance['Gene symbol'][res] + "-NTTB"             
+
+        # For all methods where coverage can be < 100%, display the %age of missing coverage
         if (data_resistance['Method'][res] == 'PARTIALX') or \
+           (data_resistance['Method'][res] == 'BLASTX') or \
            (data_resistance['Method'][res] == 'PARTIAL_CONTIG_ENDX') or \
-           ("end_of_contig" in gene) or \
-           (data_resistance['Method'][res] == 'INTERNAL_STOP') : 
-               gene += "-"+str(round(100-float(data_resistance['% Coverage of reference sequence'][res])))+"%"
-        
+           (data_resistance['Method'][res] == 'CTRL_CONTIG_END') or \
+           (data_resistance['Method'][res] == 'INTERNAL_STOP') :
+                missing_coverage = round(100-float(data_resistance['% Coverage of reference sequence'][res]),1)
+                if (100 - missing_coverage) < 100 :
+                    gene = f"{gene}-{missing_coverage}%" 
+                print(gene)
         strain = data_resistance['Name'][res]
         family = data_resistance['Class'][res]