Multi-Locus Genotypes assign

Table of Contents

• About this package
• Install
• Usage
  • Running MLG_assign with GUI
  • Running MLG_assign with command line
• Test data

About this package

Multi-Locus Genotypes (MLGs) are frequently used to carry out population genetics of clonal organisms. Tools to assign genotyped individuals to MLGs were integrated in some genetic software. However, these tools usually fail to appropriately deal with missing data. Missing data sometimes lead to potentially assign a individual genotype to several MLGs. For example, the multilocus genotype 100/200/999 (where 999 is a missing data) could be assigned to MLG 100/200/300 and to MLG 100/200/302. Despite this ambiguity, most tools assign the genotype with missing data to one or the other MLG. We developed a script that :

• group in the same MLG individuals with no missing data and with the same genotype,
• mark as unassigned individuals with missing data that could be assigned to more than one MLG.

Exemple of multilocus genotype table

	Pymrs47	Pyrms427	Pyrms657	Pyrms77B	Pyrms63	Pyrms83B	Pyrms607	Pyrms37	Pyrms233	Pyrms319	Pyrms99B	Pyrms43B
MD2249	163	211	168	200	151	115	284	197	253	284	241	350
MD2245	163	211	168	202	151	115	284	197	253	284	241	999
MD2129	163	211	168	194	151	115	284	197	253	284	241	999
MD2125	163	211	168	194	151	115	284	197	253	284	241	999
MD2124	163	211	168	194	151	115	284	197	253	284	241	999
MD1936	163	211	168	194	151	115	284	197	253	284	241	999
MD1832	163	213	168	194	151	115	284	197	253	284	241	999
MD1831	163	213	168	194	151	115	284	197	253	284	241	999
MD1826	163	213	168	194	151	115	284	197	253	284	241	999
MD1708	163	211	168	194	151	999	281	197	253	284	241	328
MD1689	163	211	168	194	151	999	278	197	253	284	241	999

Install

pip3 install MLG_assign

Usage

Running MLG_assign with GUI

• To run the gui, just call program

MLG_assign
# or
MLG_assign gui

Running MLG_assign with command line

# see help
MLG_assign cmd -h

usage: MLG_assign cmd [-h] -e <path/to/file/Excel> -s sheet name>

optional arguments:
  -h, --help            show this help message and exit

Input mandatory infos for running:
  -e <path/to/file/Excel>, --excel <path/to/file/Excel>
                        Matrix excel file
  -s sheet name>, --sheet sheet name>
                        Name of sheet in excel file

# run script
MLG_assign cmd -e Test_MLG.xlsx -s test

Test data

Data test avail at: https://github.com/sravel/MLG_assign/blob/master/Test_MLG.xlsx

wget https://github.com/sravel/MLG_assign/blob/master/Test_MLG.xlsx