Gratools functions

gratools.Graph Module

Functions

dataclass([cls, init, repr, eq, order, ...])	Returns the same class as was passed in, with dunder methods added based on the fields defined in the class.
field(*[, default, default_factory, init, ...])	Return an object to identify dataclass fields.
get_console()	Get a global Console instance.
human_sort_key(s)	Generate a sorting key for human-like sorting.
print(*objects[, sep, end, file, flush])	Print object(s) supplied via positional arguments.

Classes

BarColumn([bar_width, style, ...])	Renders a visual progress bar.
Counter([iterable])	Dict subclass for counting hashable items.
GFA(gfa_path, logger, gfa_name, version, ...)	A class to parse and process GFA files, including handling BAM files and extracting segments and links.
GratoolsBam(bam_path, threads, logger)	Class for handling BAM files.
LinkInfo(ID_plus, Orient_plus, ...)
Progress(*columns[, console, auto_refresh, ...])	Renders an auto-updating progress bar(s).
SubGraph(bam_path, bed_path, logger, ...)
TextColumn(text_format[, style, justify, ...])	A column containing text.
TimeElapsedColumn([table_column])	Renders time elapsed.
TimeRemainingColumn([compact, ...])	Renders estimated time remaining.

Class Inheritance Diagram

gratools.Gratools Module

Functions

as_completed(fs[, timeout])	An iterator over the given futures that yields each as it completes.
dataclass([cls, init, repr, eq, order, ...])	Returns the same class as was passed in, with dunder methods added based on the fields defined in the class.
field(*[, default, default_factory, init, ...])	Return an object to identify dataclass fields.
flatten(xss)
get_console()	Get a global Console instance.
human_sort_key(s)	Generate a sorting key for human-like sorting.
rmtree(path[, ignore_errors, onerror])	Recursively delete a directory tree.

Classes

BarColumn([bar_width, style, ...])	Renders a visual progress bar.
Console(*, color_system, , , , ] | None =, ...)	A high level console interface.
GFA(gfa_path, logger, gfa_name, version, ...)	A class to parse and process GFA files, including handling BAM files and extracting segments and links.
Gratools(gfa_path, threads, logger, ...)	A class to parse and process GFA files, including handling BAM files and extracting segments and links.
GratoolsBam(bam_path, threads, logger)	Class for handling BAM files.
ProcessPoolExecutor([max_workers, ...])
Progress(*columns[, console, auto_refresh, ...])	Renders an auto-updating progress bar(s).
SpinnerColumn([spinner_name, style, speed, ...])	A column with a 'spinner' animation.
SubGraph(bam_path, bed_path, logger, ...)
Table(*headers[, title, caption, width, ...])	A console renderable to draw a table.
TextColumn(text_format[, style, justify, ...])	A column containing text.

Class Inheritance Diagram

gratools.logger_config Module

Functions

configure_logger(name, log_path, verbosity)
get_console()	Get a global Console instance.
install(*[, console, width, code_width, ...])	Install a rich traceback handler.
update_logger_file_paths(logger, ...)

Classes

ColoredFormatter(fmt, datefmt, debug, verbosity)
Console(*, color_system, , , , ] | None =, ...)	A high level console interface.
Traceback([trace, width, code_width, ...])	A Console renderable that renders a traceback.

Variables

LOG_COLORS	dict() -> new empty dictionary dict(mapping) -> new dictionary initialized from a mapping object's (key, value) pairs dict(iterable) -> new dictionary initialized as if via: d = {} for k, v in iterable: d[k] = v dict(**kwargs) -> new dictionary initialized with the name=value pairs in the keyword argument list. For example: dict(one=1, two=2).
available_colors	Built-in mutable sequence.

Class Inheritance Diagram

gratools.main Module

Functions

apply_common_options(func)
configure_logger(name, log_path, verbosity)
configure_logging(func)
validate_percentage_or_int(ctx, param, value)

Variables

CONTEXT_SETTINGS	dict() -> new empty dictionary dict(mapping) -> new dictionary initialized from a mapping object's (key, value) pairs dict(iterable) -> new dictionary initialized as if via: d = {} for k, v in iterable: d[k] = v dict(**kwargs) -> new dictionary initialized with the name=value pairs in the keyword argument list. For example: dict(one=1, two=2).
LOG_LEVELS	Built-in mutable sequence.
common_options	Built-in mutable sequence.
description_tools	str(object='') -> str str(bytes_or_buffer[, encoding[, errors]]) -> str
extract_sub_graph
get_fasta
main_command
segments_info
show_chr
show_samples
specific_and_shared_segments