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.
python LINcoding -h
The necessary commands :
- allelic profiles file
-i : BIGSdb.txt #tab-separated values file
- column numbers of the selected identifiers
-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
-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
-b : 60.0,90,95.6,100 #100% is obligatory
#valeurs "int" : 60
#valeurs "float" : 60.5
Optional commands :
If Database exist :
-i new_Ecoli.txt -r BIGSdb.lin
Example
In the example folder, you have example files from the following command:
- Create DataBase LIN :
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 :
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) :
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) :
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 |