Update README.md

README.md

@@ -34,7 +34,7 @@ optional arguments:
   -h, --help       show this help message and exit
   -i FILEINPUT     (mandatory) input tab-delimited file containing the CGs associated for each isolate
   -c COLUMN_CG     (mandatory) column(s) of the selected CG(s)
-  -o FILEOUTPUT    (mandatory) output file name
+  -o FILEOUTPUT    (mandatory) basename for output files
   
 ```
 
@@ -42,10 +42,11 @@ optional arguments:
 
 The input file clustering.strain.txt inside the directory _example_ contains three columns; the first one corresponds to the strain identifiers, the next two correspond to the associated CGs. 
 
-
+The input file clustering.strain.txt in the _example_ directory contains five columns (id, isolate, ST, sublineage, clonalgroup). The id and isolate columns are the identifiers of the strains. The ST column is the 7-gene ST identifier of the corresponding isolates. The sublineage and clonalgroup columns are those to be mapped according to the ST nomenclature. 
+For this example, three files are created. The first _result.out_ is similar to the input tabulated file with the mapping of all the groups with their allocation characteristics. Two other files are created (_result.sublineage.txt_ and _result.clonalgroup.txt_), either for one for each group, a tab-delimited file with a column for the old name of the group, a second one for the name mapped to the ST, and finally its attribution.  
 
 ```bash
-python InheritanceAlgorithm.py -i clustering.strain.txt -c Seuil43,Seuil190 -o result.txt 
+python InheritanceAlgorithm.py -i clustering.strain.txt -c sublineage,clonalgroup -o result 
 ```
 
 ## References