Skip to content
Snippets Groups Projects
Select Git revision
  • bc8ff668e61571d5952773328dfc4ff49cbc97b6
  • master default protected
2 results

LINcoding

  • Clone with SSH
  • Clone with HTTPS
  • Name Last commit Last update
    example
    LINcoding.py
    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.

    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

    References