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Specific K-mer Frequency

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Source
evo-design/proto-language/proto_language/constraint/sequence_composition/specific_kmer_constraint.py
View source
Constraint contributors
Evaluate frequency or usage deviation of a specific k-mer. Supports two scoring modes:
  1. Frequency mode: Raw k-mer frequency (count / total k-mer positions).
  2. Usage deviation mode: Observed/expected ratio using a zero-order Markov model (product of individual character frequencies).
Metadata varies by mode:Frequency mode:
  • {kmer}_frequency: Float frequency value
Usage deviation mode:
  • {kmer}_usage_deviation: Float observed/expected ratio
  • {kmer}_count: Integer observed count
  • {kmer}_expected: Float expected count

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API Reference

ConfigSpecificKmerConfig Source
Configuration for evaluating a single specific k-mer.For evaluating all k-mers of a given length, use KmerFrequencyConstraint.
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string
required
The specific k-mer to evaluate (e.g., ‘CG’, ‘GATC’, ‘ATG’)
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enum
default:"frequency"
Scoring mode: ‘frequency’ for raw counts, ‘usage_deviation’ for observed/expected ratioOptions: frequency, usage_deviation
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number
required
Minimum acceptable frequency/deviation based on scoring_mode
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number
required
Maximum acceptable frequency/deviation based on scoring_mode
ReturnsConstraintOutput
One result per input sequence. The metadata field carries per-mode k-mer data (see Note).

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Usage

python

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Metadata