MLG-assign 1.0.3

Description:

MLGassign 1.0.3

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