pyplink

pyplink is a Python 3 binary Plink file parser and writer released under the MIT licence. The difference with existing parsers (and Plink itself) is that pyplink does not load the BED file in memory, making possible to work with extremely large files (e.g. 1000 Genomes Phase 3 files).

For more information on how to use pyplink, refer to the API documentation. Below is a snippet describing the most common usage of the module.

from pyplink import PyPlink

with PyPlink("plink_file_prefix") as bed:
    # Getting the BIM and FAM
    bim = bed.get_bim()
    fam = bed.get_fam()

    # Iterating over all loci
    for loci_name, genotypes in bed:
        pass

    # Getting the genotypes of a single marker (numpy.ndarray)
    genotypes = bed.get_geno_marker("rs12345")