MSA Generator

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Source

evo-design/proto-language/proto_language/generator/msa_generator.py

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Generator contributors

Generator that samples mutations from MSA position-specific distributions. This generator computes empirical probability distributions for each position in a multiple sequence alignment, then mutates proposal sequences by sampling from these distributions.

API Reference

ConfigMSAGeneratorConfig Source

Configuration object for MSAGenerator.This class defines configuration parameters for the MSA generator, which samples mutations from position-specific probability distributions derived from a multiple sequence alignment.

MSA

required

Multiple sequence alignment (list of aligned sequences).

integer

default:"1"

Number of positions to mutate per sample

boolean

default:"False"

Whether to include gaps when calculating position probabilities

Usage

python

>>> from proto_language.generator import MSAGenerator, MSAGeneratorConfig
>>> from proto_language.core import Segment
>>> from proto_tools.entities.msa import MSA
>>> config = MSAGeneratorConfig(
...     msa=MSA(aligned_sequences=["MVLS", "AVLS", "MVLS"]),
...     num_mutations=1,
... )
>>> gen = MSAGenerator(config)
>>> segment = Segment(sequence="MVLS", sequence_type="protein")
>>> gen.assign(segment)
>>> gen.sample()  # Position 0 has 2/3 chance of M, 1/3 chance of A

Metadata

Property	Value
Key	`msa`
Class	`MSAGenerator`
Category	`mutation`
Input Type	`starting_sequence`
Uses GPU	`False`
Supported Sequence Types	All
Allows Empty Start	`False`

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MSA Generator

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