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.
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
1 maintainer
Metadata
1 maintainer
Release files for MLG-assign 1.0.3
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| MLG_assign-1.0.3-py2.py3-none-any.whl | Python 2, Python 3 | none | any | Details |
Release files / MLG_assign-1.0.3-py2.py3-none-any.whl
| Download URL | MLG_assign-1.0.3-py2.py3-none-any.whl |
|---|---|
| Size | 15.1 kB |
| Tags | Python 2 Python 3 |
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