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:
- 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:
- 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:
- 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:
- 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:
- 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:
- process_struct(struct_name: str, struct: str, svg_path: Path, png_path: Path, script_file: Path, keep_tmp: bool, force: bool)
Render a single RNA structure using RNArtistCore.
- Parameters:
struct_name (
str) – Name string for this structure (used in the Jinja template and as the RNArtist structure identifier).struct (
str) – Dictionary with keys"seq"and"value"describing the structure.svg_path (
Path) – Destination path for the rendered SVG file.png_path (
Path) – Destination path for the rendered PNG file.script_file (
Path) – Path at which to write the temporary KTS script.keep_tmp (
bool) – Whether to retain the KTS script after rendering.force (
bool) – Whether to overwrite existing output files.
- Returns:
Paths of the output files that were written.
- Return type:
list[Path]
- 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)
Build a JinjaData object for rendering an RNArtist script.
- Parameters:
struct (
str) – Dictionary with keys"seq"(sequence) and"value"(dot-bracket string) describing the RNA structure.color_dict (
dict) – Mapping of 1-based position to reactivity value for coloring.name (
str) – Name of the structure, used as the RNArtist structure name.out_dir (
Path) – Output directory for the rendered image files.draw_svg (
bool) – Whether to render an SVG image.draw_png (
bool) – Whether to render a PNG image.highlight_pos (
Iterable[int], optional) – Positions to highlight in green (e.g. edited positions).
- Returns:
Data object suitable for rendering with the RNArtist Jinja template.
- Return type:
- 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] = Sentinel.UNSET, *, 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’]