Add README.md

README.md

+# LINcoding
+
+This software allows from an allelic profiles to create LIN codes.
+
+-------------------------
+## Installation
+
+#### Requirements
+
+This tool is developed in Python3. 
+It uses numpy, copy, argparse, itertools, random and re library.
+
+## How does it work ?
+
+Please, read the help message for advanced features on the tool.
+
+```bash
+LINcoding -h
+```
+___
+ #### The necessary commands :
+ 
+- allelic profiles file
+
+```bash
+ -i : BIGSdb.txt #tab-separated values file
+```
+
+- column numbers of the selected identifiers
+
+```bash
+ -t : 1-2 #column 1 to 2 
+ #or 
+ -t : 1,5 #column 1 and 5 
+ #or 
+ -t : 1-3,5 #column 1 to 3 and 5
+```
+- column numbers of the chosen alleles
+
+```bash
+ -l : 3- #column 3 to all others 
+  #or 
+ -l : 3-15 #column 3 to 15
+  #or 
+ -l : 5-10,206 #column 5 to 10 and 206
+```
+
+ - set of thresholds (in percentage) if -i does not exist
+
+```bash
+ -b : 60.0,90,95.6,100 #100% is obligatory 
+ #valeurs "int" :  60 
+ #valeurs "float" : 60.5 
+```
+
+___
+ #### Optional commands :
+If Database exist : 
+ 
+```bash
+-i new_Ecoli.txt -r BIGSdb.lin
+```
+
+## Example
+
+In the example folder, you have example files from the following command:
+
+- Create DataBase LIN :  
+
+```bash
+python LINcode.py -i BIGSdb.txt -t 1-2 -l 3- -b 1,20,45,66,80,90,95,96,98,99,100
+```
+
+- Update DataBase LIN :
+
+```bash         
+python LINcode.py -i new_Ecoli.txt -r BIGSdb.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 
+```
+
+- 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 
+```
+
+## Output files
+
+- Output 
+
+Name | content |
+---- | ------- |
+BIGSdb.lin | LIN Database |
+LIN_BIGSdb.txt| LIN Isolates List |
+ 
+- Option (-tree or -lg)
+
+ Name | content |
+----  | ------- |
+ARBRE_REF.txt |  tree with length of branches |
+Arbres.txt|  tree without length of branches|
+
+
+## References