Reference

Constants

barcode_pattern	str(object='') -> str str(bytes_or_buffer[, encoding[, errors]]) -> str
genome_metadata_names	Built-in immutable sequence.
lane_pattern	str(object='') -> str str(bytes_or_buffer[, encoding[, errors]]) -> str
metadata_denylist	Built-in immutable sequence.
metrics_cols	Built-in immutable sequence.
update_message	str(object='') -> str str(bytes_or_buffer[, encoding[, errors]]) -> str

Math and statistics

euclidean	Compute the Euclidean distance between two vectors.
fold_change_to_log_ratio	Convert fold change to log ratio.
geometric_mean	Compute the geometric mean.
headtail	Return (and print) the first and last n elements / rows.
intersect_all	Return the intersection of multiple sequences.
intersection_matrix	Build a Boolean intersection matrix.
log_ratio_to_fold_change	Convert log ratio to fold change.
ranked_matrix	Rank values within each column, with ties averaged.
sem	Compute the standard error of the mean.
zscore	Compute Z-scores (column-wise for matrices).

Data manipulation

dupes	Return duplicated elements.
keep_only_atomic_cols	Keep only columns that contain scalar (atomic) values.
match_all	Return indices of all matches of x in table.
match_nested	Recursively search for x in a nested dict/list structure.
not_dupes	Return elements that appear exactly once.

String utilities

str_extract	Extract first match of pattern from string.
str_extract_all	Return all matches of pattern in string.
str_match	Return the first regex match object of pattern in string.
str_match_all	Return all regex match objects for pattern in string.
str_pad	Pad a string to a minimum width.
str_remove_empty	Remove empty strings and None values from a list.
str_replace_na	Replace None values with a placeholder string.
str_split	Split string by a regex pattern.
print_string	Coerce an object to a human-friendly print string.
truncate_string	Truncate string to n characters, appending '...' if needed.

File and path utilities

basename_sans_ext	Return the file basename without extension(s).
compress	Compress a file.
decompress	Decompress a file.
file_depth	Return the directory depth of path.
file_ext	Return the file extension(s) including compression suffix.
init_dir	Create a directory (and parents) if it does not exist.
parent_dir	Return the n-th parent directory of path.
parent_directory	Return the n-th parent directory of path.
realpath	Resolve path to an absolute real path.
tempdir2	Create a unique temporary directory.
unlink2	Delete a file or directory tree.

Path string manipulation

add_to_path_end	Append new_path to the end of a path string (if not present).
add_to_path_start	Prepend new_path to the start of a path string (if not present).
collapse_to_path_string	Join paths into a single colon-separated string.
remove_from_path	Remove target from a path string.
split_path_string	Split a colon-separated path string.
unique_path_string	Remove duplicate entries from a path string.

System utilities

cpus	Return available CPU count, capped at n if requested.
git_current_branch	Return the name of the current Git branch.
git_default_branch	Return the default branch name of the Git repository.
quietly	Suppress console output and warnings within a block.
ram	Return total system RAM in gibibytes (GiB).
random_string	Generate a random alphanumeric string of length n.
shell	Run a shell command.

Version utilities

major_minor_version	Return major.minor from a version string.
major_version	Return the major component of a version string.
minor_version	Return major.minor from a version string.
sanitize_version	Normalise a version string using PEP 440.

Download and URL

download	Download a file from url.
paste_url	Join URL parts with /.

Display and cache helpers

show_header	Return a formatted header line.
show_slot_info	Return a formatted summary of an object's attributes.
simple_class	Return the simple class name (without module path).
pkg_cache_dir	Return (and create) a package-specific cache directory.