actio_python_utils.utils

Functions

cast_chromosome_to_int(chromosome)	Cast a chromosome string, optionally prefixed with chr, to an integer.
check_valid_output_directory(output_directory)	Check if the given directory is valid for outputting.
coalesce(*args)	Return the first argument that is not None
debug(func)	Wraps a function to output the function signature, run the function, output the return value, and return the return value.
extract_excel_sheet(fn, output_fn[, sheet, ...])	Extract a sheet from an Excel spreadsheet.
flatten_cfg(key[, d, sep])	Flatten a nested value in a dict
get_csv_fields(fn[, sep, sanitize, ...])	Get the column names from the first line of the specified file and optionally replaces an arbitrary sequence of strings to others
open_bz2(filename[, mode, buff, external])	Return a file handle to filename using pbzip2, bzip2, or b2 module
open_gz(filename[, mode, buff, external])	Return a file handle to filename using pigz, gzip, or gzip module
open_pipe(command[, mode, buff])	Runs a subprocess.Popen and either retains input or output
open_xz(filename[, mode, buff, external])	Return a file handle to filename using either xz or lzma module
rename_dict_keys(original_dict, renames)	Returns a new dict that's a copy of the supplied dict but with an arbitrary number of keys renamed
sync_to_s3(dir_name, s3_path)	Syncs a directory to specific S3 bucket/path.
timer(func)	Wraps a function to output the running time of function calls.
which(program)	type program: str
zopen(filename[, mode, buff, external])	Open pipe, zipped, or unzipped file automagically

Classes

CustomCSVDialect()
DictToFunc(choices)	Class that after initializing with a dict can be called to map keys to values, e.g..
NumericValue([min_value, max_value, ...])	Creates a class that can be used as a function to verify that a passed argument is a numeric value of the correct type and in the expected range