AAlogo

class AAlogo(logo_type='probability')[source]

Bases: object

Amino Acid logo (AAlogo) class for computing sequence logo matrices and conservation scores.

Sequence logos visualize the amino acid composition and conservation at each residue position. AAlogo computes logo matrices from sequence parts using the logomaker [Tareen20] package. Conservation is summarized per position (get_df_logo_info()) or as a single scalar (get_conservation()).

Added in version 1.0.3.

Parameters:: logo_type (Literal[‘probability’, ‘weight’, ‘counts’, ‘information’])

Methods

`get_conservation`(df_logo_info[, value_type])	Summarize per-position information content into a single conservation score.
`get_df_logo`(df_parts[, labels, label_test, ...])	Compute a sequence logo matrix for the provided sequence parts.
`get_df_logo_info`(df_parts[, labels, ...])	Compute per-position information content (in bits) from sequence parts.

__init__(logo_type='probability')[source]

Parameters:

logo_type ({'probability', 'weight', 'counts', 'information'}, default='probability') –

Type of sequence logo encoding:

probability: Normalized probability distribution of amino acids per position.
weight: Weighted (log-odds) representation.
counts: Raw amino acid counts per position.
information: Information content in bits per position.