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.
Common functionality to support testing in skbio.
get_data_path(fn[, subfolder]) |
Return path to filename fn in the data folder. |
TestRunner(filename) |
Simple wrapper class around nosetests functionality. |
assert_ordination_results_equal(left, right) |
Assert that ordination results objects are equal. |
assert_data_frame_almost_equal(left, right) |
Raise AssertionError if pd.DataFrame objects are not “almost equal”. |
Generally useful functions that don’t fit in more specific locations.
cardinal_to_ordinal(n) |
Return ordinal string version of cardinal int n. |
create_dir(dir_name[, fail_on_exist, ...]) |
Create a directory safely and fail meaningfully |
find_duplicates(iterable) |
Find duplicate elements in an iterable. |
is_casava_v180_or_later(header_line) |
Check if the header looks like it is Illumina software post-casava v1.8 |
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 |
EfficiencyWarning |
Warn about potentially accidental use of inefficient code. |
RepresentationWarning |
Warn about assumptions made for the successful completion of a process. |