diff --git a/README.md b/README.md index ba2e75b06df96c9508aa2c6ee1d888207080acfb..3fd38f6e7185cb4a21ab744d2a9f7a84024b0c1f 100644 --- a/README.md +++ b/README.md @@ -73,26 +73,26 @@ In the example folder, you have example files from the following command: - Create DataBase LIN : ```bash -python LINcode.py -i BIGSdb_eliza.txt -t 1-2 -l 3- -b 10,20,50,80,95,99.68,99.74,99.81,99.87,99.94,100 +python LINcode.py -i BIGSdb_eliza.txt -t 1-2 -l 3- -b 10,20,50,80,99.68,99.74,99.81,99.87,99.94,100 ``` - Update DataBase LIN : ```bash -python LINcode.py -i new_Ecoli.txt -r BIGSdb_eliza.txt -t 1-2 -l 3- +python LINcode.py -i BIGSdb_eliza_update.txt -r BIGSdb_eliza.lin -t 1-2 -l 3- ``` _______________________________________________________________________________ - Create DataBase LIN + prefix tree without length of branches (newick) : ```bash -python LINcode.py -i BIGSdb.txt -t 1-2 -l 3- -b 1,20,45,66,80,90,95,96,98,99,100 -tree Y +python LINcode.py -i BIGSdb_eliza.txt -t 1-2 -l 3- -b 10,20,50,80,99.68,99.74,99.81,99.87,99.94,100 -tree Y ``` - Create DataBase LIN + prefix tree with length of branches (newick) : ```bash -python LINcode.py -i BIGSdb.txt -t 1-2 -l 3- -b 1,20,45,66,80,90,95,96,98,99,100 -tree Y -lg Y +python LINcode.py -i BIGSdb_eliza.txt -t 1-2 -l 3- -b 10,20,50,80,99.68,99.74,99.81,99.87,99.94,100 -tree Y -lg Y ``` ## Output files @@ -101,8 +101,8 @@ python LINcode.py -i BIGSdb.txt -t 1-2 -l 3- -b 1,20,45,66,80,90,95,96,98,99,100 Name | content | ---- | ------- | -BIGSdb.lin | LIN Database | -LIN_BIGSdb.txt| LIN Isolates List | +BIGSdb_eliza.lin | LIN Database | +LIN_BIGSdb_eliza.txt| LIN Isolates List | - Option (-tree or -lg)