Matis_plink

Description

plinkPy takes .ped and .map files exported from Plink as input. After parsing of both files into a single object in an OOP-manner, it allows to extract part of the data and export it back into .ped and .map files as well as csv, genepop and structure formats.

Getting started

When the plinkPy.py file is in the working directory with an empty __init__.py file:

from plinkPy import *

Input

The .ped .map input should display A/B alleles with 0 as the missing value.

Usage

Create the plinkPy instance and parse the files

plink_1 = plinkPy('plink_export.ped', 'plink_export.map')

Access properties

Get the individuals as well as their number:

plink_1.individuals

Get the markers as well as their number:

plink_1.markers

Filter

By a list of individuals target_1:

individuals_of_interest = plink_1.get_individuals(target_1)

By a list of markers target_2:

markers_of_interest = plink_1.get_markers(target_2)

Export

individuals_of_interest.export(format, 'filtered_export')

The format can be:

• 'ped_map'
• 'csv'
• 'genepop'
• 'structure'

Export to csv, genepop and structure changes the original order of markers into an alphabetic one.

Export to genepop and structure adds an empty blank line at the end of the file.

Export to genepop misses a blank space after the comma at individual lines.

Export to structure codes missing value as 9.