snpio.GenotypeEncoder

class snpio.GenotypeEncoder(genotype_data)[source]

Encode genotypes to various formats suitable for machine learning.

This class provides methods to encode genotypes to various formats suitable for machine learning, including 012, one-hot, and integer encodings, as well as the inverse operations.

Example

>>> # Import necessary modules
>>> from snpio import VCFReader, GenotypeEncoder
>>>
>>> # Initialize VCFReader and GenotypeEncoder objects
>>> gd = VCFReader(filename="my_vcf.vcf", popmapfile="my_popmap.txt")
>>> ge = GenotypeEncoder(gd)
>>>
>>> # Encode genotypes to 012, one-hot, and integer formats
>>> gt_012 = ge.genotypes_012
>>> gt_onehot = ge.genotypes_onehot(gt_012)
>>> gt_int = ge.genotypes_int(gt_012)
>>>
>>> # Inverse operations
>>> ge.genotypes_012 = gt_012
>>> ge.genotypes_onehot = gt_onehot
>>> ge.genotypes_int = gt_int

plot_format

Plot format for the data.

Type:: str

prefix

Prefix for the output directory.

Type:: str

verbose

If True, display verbose output.

Type:: bool

snp_data

List of lists of SNPs.

Type:: List[List[str]]

samples

List of sample IDs.

Type:: List[str]

filetype

File type of the data.

Type:: str

missing_vals

List of missing values.

Type:: List[str]

replace_vals

List of values to replace missing values with.

Type:: List[str]

__init__(genotype_data)[source]

Initialize the GenotypeEncoder object.

This class provides methods to encode genotypes to various formats suitable for machine learning, including 012, one-hot, and integer encodings, as well as the inverse operations.

Parameters:: genotype_data (GenotypeData) – Initialized GenotypeData object.

Note

The GenotypeData object must be initialized before creating an instance of this class.

Methods

`__init__`(genotype_data)	Initialize the GenotypeEncoder object.
`convert_012`(snps)	Convert genotype strings to 012 encoding.
`convert_int_iupac`(snp_data[, encodings_dict])	Convert input data to integer-encoded format (0-9) based on IUPAC codes.
`convert_onehot`(snp_data[, encodings_dict])	Convert input data to one-hot encoded format.
`decode_012`(X[, is_nuc])	Decode 012 encodings to IUPAC characters with metadata repair.
`decode_alleles_two_channel`(allele1, allele2)	Convert two integer allele matrices back into IUPAC-encoded genotypes.
`encode_alleles_two_channel`(snp_data)	Convert IUPAC genotypes to two integer allele matrices.
`inverse_int_iupac`(int_encoded_data[, ...])	Convert integer-encoded data back to original format.
`inverse_onehot`(onehot_data[, encodings_dict])	Convert one-hot encoded data back to original format.

Attributes

`genotypes_012`	Encode 012 genotypes as a numpy array.
`genotypes_int`	Integer-encoded (0-9 including IUPAC characters) snps format.
`genotypes_onehot`	One-hot encoded snps format of shape (n_samples, n_loci, 4).
`two_channel_alleles`	Two-channel allele matrices.