seismicrna.draw package

Submodules

class seismicrna.draw.draw.ColorBlock(color_type: str, color_value: str, color_to: str = None, color_filter: str = None, location: tuple[int] = None)

Bases: object

to_dict()

class seismicrna.draw.draw.JinjaData(path_: Path, seq: str, value: str, name: str, color_dict: dict, details_value: int, color_blocks: list[ColorBlock], draw_svg: bool, draw_png: bool)

Bases: object

to_dict()

class seismicrna.draw.draw.RNArtistRun(report_file: Path, tmp_dir: Path, struct_num: Iterable[int], color: bool, verify_times: bool, draw_svg: bool, draw_png: bool, update: bool, num_cpus: int)

Bases: object

property best_struct

property color_dict

property edited_numbers

get_ct_file(top: Path)

Get the path to the connectivity table (CT) file.

Parameters:: top (pathlib.Path) – Top-level directory.
Returns:: Path of the file.
Return type:: pathlib.Path

get_db_file(top: Path)

Get the path to the dot-bracket (DB) file.

Parameters:: top (pathlib.Path) – Top-level directory.
Returns:: Path of the file.
Return type:: pathlib.Path

get_png_file(top: Path, struct: int)

Get the path to the PNG file.

Parameters:: top (pathlib.Path) – Top-level directory.
Returns:: Path of the file.
Return type:: pathlib.Path

get_script_file(top: Path, struct: int)

Get the path to the RNArtist script (.kts) file.

Parameters:: top (pathlib.Path) – Top-level directory.
Returns:: Path of the file.
Return type:: pathlib.Path

get_svg_file(top: Path, struct: int)

Get the path to the SVG file.

Parameters:: top (pathlib.Path) – Top-level directory.
Returns:: Path of the file.
Return type:: pathlib.Path

get_varna_color_file(top: Path)

Get the path to the VARNA color file.

Parameters:: top (pathlib.Path) – Top-level directory.
Returns:: Path of the file.
Return type:: pathlib.Path

process_struct(struct_name: str, struct: str, svg_path: Path, png_path: Path, script_file: Path, keep_tmp: bool, force: bool)

run(keep_tmp: bool, force: bool)

property table

property table_class

property table_classes

property table_file

property table_loader

seismicrna.draw.draw.build_jinja_data(struct: str, color_dict: dict, name: str, out_dir: Path, draw_svg: bool, draw_png: bool, highlight_pos: Iterable[int] = None)

seismicrna.draw.draw.draw(report_path: Path, *, struct_num: Iterable[int], color: bool, draw_svg: bool, draw_png: bool, update: bool, tmp_dir: Path, keep_tmp: bool, verify_times: bool, num_cpus: int, force: bool = False): Draw RNA structure(s) from a FoldReport.

seismicrna.draw.draw.parse_color_file(file_path)

seismicrna.draw.main.run(input_path: Iterable[str | Path], *, struct_num: Iterable[int] = (), color: bool = True, draw_svg: bool = True, draw_png: bool = False, update_rnartistcore: bool = False, force: bool = False, num_cpus: int = 4, verify_times: bool = True, keep_tmp: bool = False, tmp_pfx='./tmp') → list[Path]

Draw RNA structures with reactivities using RNArtistCore.

Parameters:

struct_num (Iterable) – Draw the specified structure (zero-indexed) or -1 for all structures. By default, draw the structure with the best AUROC. [keyword-only, default: ()]
color (bool) – Color bases by their reactivity [keyword-only, default: True]
draw_svg (bool) – Output each drawing in a Scalable Vector Graphics file [keyword-only, default: True]
draw_png (bool) – Output each drawing in a Portable Network Graphics file [keyword-only, default: False]
update_rnartistcore (bool) – Check for and install updates to RNArtistCore. [keyword-only, default: False]
force (bool) – Force all tasks to run, overwriting any existing output files [keyword-only, default: False]
num_cpus (int) – Use up to this many CPUs simultaneously [keyword-only, default: 4]
verify_times (bool) – Verify that report files from later steps have later timestamps [keyword-only, default: True]
keep_tmp (bool) – Keep temporary files after finishing [keyword-only, default: False]
tmp_pfx – Write all temporary files to a directory with this prefix [keyword-only, default: ‘./tmp’]