pyplink’s API

class pyplink.PyPlink(prefix, mode='r', bed_format='SNP-major')

Reads and store a set of binary Plink files.

Parameters:

• prefix (str) – The prefix of the binary Plink files.

• mode (str) – The open mode for the binary Plink file.

• bed_format (str) – The type of bed (SNP-major or INDIVIDUAL-major).

Reads or write binary Plink files (BED, BIM and FAM).

from pyplink import PyPlink

# Reading BED files
with PyPlink("plink_file_prefix") as bed:
    pass

# Writing BED files
with PyPlink("plink_file_prefix", "w") as bed:
    pass

close()

Closes the BED file.

get_acgt_geno_marker(marker)

Gets the genotypes for a given marker (ACGT format).

Parameters:

marker (str) – The name of the marker.

Returns:

The genotypes of the marker (ACGT format).

Return type:

numpy.ndarray

get_bim()

Returns the BIM file.

Returns:

The BIM file.

Return type:

pandas.DataFrame

get_duplicated_markers()

Returns the duplicated markers, if any.

Returns:

The set of duplicated marker (might be empty).

Return type:

dict

get_fam()

Returns the FAM file.

Returns:

The FAM file.

Return type:

pandas.DataFrame

get_geno_marker(marker, return_index=False)

Gets the genotypes for a given marker.

Parameters:

• marker (str) – The name of the marker.

• return_index (bool) – Wether to return the marker’s index or not.

Returns:

The genotypes of the marker (additive format).

Return type:

numpy.ndarray

get_nb_markers()

Returns the number of markers.

Returns:

The number of markers in the dataset.

Return type:

int

get_nb_samples()

Returns the number of samples.

Returns:

The number of samples in the dataset.

Return type:

int

iter_acgt_geno()

Iterates over genotypes (ACGT format).

Returns:

The name of the marker as a string, and its genotypes as a numpy.ndarray (ACGT format).

Return type:

tuple

iter_acgt_geno_marker(markers)

Iterates over genotypes for a list of markers (ACGT format).

Parameters:

markers (list) – The list of markers to iterate onto.

Returns:

The name of the marker as a string, and its genotypes as a numpy.ndarray (ACGT format).

Return type:

tuple

iter_geno()

Iterates over genotypes from the beginning of the BED file.

Returns:

The name of the marker as a string, and its genotypes as a numpy.ndarray (additive format).

Return type:

tuple

iter_geno_marker(markers, return_index=False)

Iterates over genotypes for a list of markers.

Parameters:

• markers (list) – The list of markers to iterate onto.

• return_index (bool) – Wether to return the marker’s index or not.

Returns:

The name of the marker as a string, and its genotypes as a numpy.ndarray (additive format).

Return type:

tuple

next()

Returns the next marker.

Returns:

The marker name as a string and its genotypes as a numpy.ndarray.

Return type:

tuple

seek(n)

Gets to a certain marker position in the BED file.

Parameters:

n (int) – The index of the marker to seek to.

write_genotypes(genotypes)

Write genotypes to binary file.

Parameters:

genotypes (numpy.ndarray) – The genotypes to write in the BED file.

A module to read Plink’s binary files.

pyplink.test(verbosity=1)

Executes all the tests for pyplink.

Parameters:

verbosity (int) – The verbosity level for unittest.

Just set verbosity to an integer higher than 1 to have more information about the tests.