From 2de921cd9608c039bad986446b25acc0b898e8a1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?M=C3=A9lanie=20=20HENNART?= <melanie.hennart@pasteur.fr> Date: Wed, 30 May 2018 10:52:15 +0200 Subject: [PATCH] Update README.md --- README.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index ba2e75b..3fd38f6 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) -- GitLab