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Kmers utils

kmers_utils

This module provides utility functions for working with k-mers.

Contents
  • kmers_difference: Calculate the difference in k-mers between two defaultdicts.
  • kmers_intersections: Calculate the intersection in k-mers between two defaultdicts.

Note: This module assumes that the input sequence contains characters from the DNA alphabet ('ACTG') by default. Custom alphabets can be specified using the 'dictionary' parameter.

Todo
  • Implement tests.

kmers_difference(seq_kmers, ref_kmers)

Calculate the difference in k-mers between two defaultdicts.

This function takes two defaultdicts containing k-mers and their frequency positions counts, calculates the k-mer differences between them, and returns a list of k-mers that are present in the 'seq_kmers' defaultdict but not in the 'ref_kmers' defaultdict.

Parameters:

Name Type Description Default
seq_kmers defaultdict

A defaultdict mapping k-mers to their frequency counts in the sequence data.

 required
ref_kmers defaultdict

A defaultdict mapping k-mers to their frequency counts in the reference data.

 required

Returns:

Type Description
list[str]

list[str]: A list of k-mers present in 'seq_kmers' but not in 'ref_kmers'.
Source code in python/gramep/kmers_utils.py 
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def kmers_difference(
    seq_kmers: defaultdict, ref_kmers: defaultdict
) -> list[str]:
    """
    Calculate the difference in k-mers between two defaultdicts.

    This function takes two defaultdicts containing k-mers and their frequency positions counts,
    calculates the k-mer differences between them, and returns a list of k-mers that
    are present in the 'seq_kmers' defaultdict but not in the 'ref_kmers' defaultdict.

    Args:
        seq_kmers (defaultdict): A defaultdict mapping k-mers to their frequency counts
                                 in the sequence data.
        ref_kmers (defaultdict): A defaultdict mapping k-mers to their frequency counts
                                 in the reference data.

    Returns:
        list[str]: A list of k-mers present in 'seq_kmers' but not in 'ref_kmers'.
    """
    seq = set(seq_kmers)
    ref = set(ref_kmers)
    return list(seq - ref)

kmers_intersections(seq_kmers, ref_kmers)

Calculate the intersection in k-mers between two defaultdicts.

This function takes two defaultdicts containing k-mers and their frequency positions counts, calculates the k-mer intersection between them, and returns a list of k-mers that are present in both defaultdicts.

Parameters:

Name Type Description Default
seq_kmers defaultdict

A defaultdict mapping k-mers to their frequency counts in the sequence data.

 required
ref_kmers defaultdict

A defaultdict mapping k-mers to their frequency counts in the reference data.

 required

Returns:

Type Description
list[str]

list[str]: A list of k-mers present in both defaultdicts.
Source code in python/gramep/kmers_utils.py 
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def kmers_intersections(
    seq_kmers: defaultdict, ref_kmers: defaultdict
) -> list[str]:
    """
    Calculate the intersection in k-mers between two defaultdicts.

    This function takes two defaultdicts containing k-mers and their frequency positions counts,
    calculates the k-mer intersection between them, and returns a list of k-mers that
    are present in both defaultdicts.

    Args:
        seq_kmers (defaultdict): A defaultdict mapping k-mers to their frequency counts
                                 in the sequence data.
        ref_kmers (defaultdict): A defaultdict mapping k-mers to their frequency counts
                                 in the reference data.

    Returns:
        list[str]: A list of k-mers present in both defaultdicts.
    """
    seq = set(seq_kmers)
    ref = set(ref_kmers)

    return list(seq.intersection(ref))