mkt.databases.plot.SequenceAlignment

class mkt.databases.plot.SequenceAlignment(list_sequences: list[str], list_ids: list[str], dict_colors: dict[str, str], font_size: int = 9, plot_width: int = 800, plot_height: int = None, bool_top: bool = True, bool_reverse: bool = True, bool_gridplot: bool = True)[source]

Bases: object

Class for sequence alignment plot.

__init__(*args: Any, **kwargs: Any) → None

Methods

`__eq__`(other)	Return self==value.
`__post_init__`()
`create_coldatasource`()
`generate_bottom_plot`()	Generate sequence alignment plot adapted from https://dmnfarrell.github.io/bioinformatics/bokeh-sequence-aligner.
`generate_gridplot`()	Generate sequence alignment gridplot.
`generate_top_plot`()	Generate sequence alignment plot adapted from https://dmnfarrell.github.io/bioinformatics/bokeh-sequence-aligner.
`get_colors`(list_str, dict_colors)	Get colors for residue in a given sequence.
`show_plot`()	Show sequence alignment plot via Bokeh in separate window.

Attributes

`__dataclass_fields__`
`__dataclass_params__`
`__match_args__`
`__pydantic_config__`
`bool_gridplot`	Use gridplot or not.
`bool_reverse`	Reverse the sequence or not.
`bool_top`	Show entire sequence view on top or not (no text, with zoom).
`font_size`	Font size for alignment.
`plot_height`	Height of the plot; default None and will full-page heuristic.
`plot_width`	Width of the plot.
`list_sequences`	List of sequences to show in aligner.
`list_ids`	List of sequence IDs.
`dict_colors`	Dictionary of colors for each sequence.

bool_gridplot: bool = True: Use gridplot or not.

bool_reverse: bool = True: Reverse the sequence or not.

bool_top: bool = True: Show entire sequence view on top or not (no text, with zoom).

create_coldatasource()[source]

dict_colors: dict[str, str]: Dictionary of colors for each sequence.

font_size: int = 9: Font size for alignment.

generate_bottom_plot() → None[source]: Generate sequence alignment plot adapted from https://dmnfarrell.github.io/bioinformatics/bokeh-sequence-aligner.

generate_gridplot() → None[source]: Generate sequence alignment gridplot.

generate_top_plot() → None[source]: Generate sequence alignment plot adapted from https://dmnfarrell.github.io/bioinformatics/bokeh-sequence-aligner.

static get_colors(list_str: str, dict_colors: dict[str, str]) → list[str][source]

Get colors for residue in a given sequence.

Parameters:

list_str (str) – List of residues in a sequence.
dict_colors (dict[str, str]) – Dictionary of colors for each residue.

Returns:

List of colors for each residue.

Return type:

list[str]

list_ids: list[str]: List of sequence IDs.

list_sequences: list[str]: List of sequences to show in aligner.

plot_height: int = None: Height of the plot; default None and will full-page heuristic.

plot_width: int = 800: Width of the plot.

show_plot() → None[source]: Show sequence alignment plot via Bokeh in separate window.