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Application to add MLG

Project description

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 lead 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 dat 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

# see help
MLG_assign -h

Input infos not mandatory:
  -v, --version         Use if you want to know which version of
                        MLGassign.py you are using
  -h, --help            show this help message and exit
  -d, --debug           enter verbose/debug mode

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 -e Test_MLG.xlsx -s test

Test data

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

Project details


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