/MLG_assign

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.

Primary LanguagePythonGNU General Public License v3.0GPL-3.0

Multi-Locus Genotypes assign

Table of Contents

About this package

Python /3.7+ PyPi MLG-assign

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