Core

This module provides a high-level interface for working with metric dataframes, e.g., manipulating, visualizing and saving a metric dataframe.

Base Components

Core objects and classes that define the seqme evaluation and metric API.

seqme.evaluate	Compute a set of metrics for multiple sequence groups.
seqme.Cache	Caches model-generated feature representations of sequences.
seqme.Metric	Abstract base class for defining a metric.
seqme.MetricResult	Data structure to store a metric result.

Data Manipulation

Utility functions to combine, filter, and reorganize metric dataframes.

seqme.combine	Combine multiple metric dataframes into a single metric dataframe.
seqme.rank	Calculate the non-dominated rank of each entry using one or more metrics.
seqme.extract_non_dominated	Extract the non-dominated rows using one or more metrics.
seqme.top_k	Extract top-k rows of the metric dataframe based on a metrics values.
seqme.sort	Sort the metric dataframe by a metrics values.
seqme.strip	Strip deviations from metrics in the metric dataframe.
seqme.rename	Rename one or more metrics in the metric dataframe.

Visualization

Functions for visual exploration and presentation of metric dataframes.

seqme.show	Display a metric dataframe as a styled table.
seqme.plot_bar	Plot a bar chart for a given metric with optional error bars.
seqme.plot_scatter	Plot a scatter plot for two metrics with optional error rectangles or bars.
seqme.plot_parallel	Plot a parallel coordinates plot where each coordinate is a metric.
seqme.plot_line	Plot a series for a given metric across multiple iterations/steps with optional error bars.
seqme.to_latex	Export a metric dataframe to a LaTeX table.

Input / Output

Functions for serializing and loading sequences, cache and metric dataframes.

seqme.to_pickle	Serialize an object and write it to a pickle file.
seqme.read_pickle	Load and return an object from a pickle file.
seqme.to_fasta	Write sequences to a FASTA file.
seqme.read_fasta	Retrieve sequences from a FASTA file.