Utility functionality (skbio.util)

This package provides general exception/warning definitions used throughout scikit-bio, as well as various utility functionality, including I/O and unit-testing convenience functions.

Testing functionality

Common functionality to support testing in skbio.

get_data_path(fn[, subfolder]) Return path to filename fn in the data folder.

Miscellaneous functionality

Generally useful functions that don’t fit in more specific locations.

create_dir(dir_name[, fail_on_exist, ...]) Create a directory safely and fail meaningfully
flatten(items) Removes one level of nesting from items
remove_files(list_of_filepaths[, ...]) Remove list of filepaths, optionally raising an error if any are missing
safe_md5(open_file[, block_size]) Computes an md5 sum without loading the file into memory
is_casava_v180_or_later(header_line) Check if the header looks like it is Illumina software post-casava v1.8

Exceptions

FileFormatError Exception raised when a file can not be parsed.
RecordError Exception raised when a record is bad.
FieldError Exception raised when a field within a record is bad.

Warnings

EfficiencyWarning Warn about potentially accidental use of inefficient code.