dasi.utils

Functions

bisect_between(a, low, high)	Returns the start (inclusive) and end (exclusive) indices for a sorted array using a key function.
bisect_slice_between(a, keys, low, high)	Slice the iterable using inclusive bisection.
group_by(arr, key)	Group a list by some key.
log_metadata([key, class_attribute, …])	wrapper for logging method run times for a class.
log_times([key, class_attribute])	wrapper for logging method run times for a class.
perfect_subject(data)	Determine whether a blast result consumes the entire subject.
sort_with_keys(a, key)	Sort an iterable, returning both the sorted array and the sorted keys.

Utilities (dasi.utils)

This module provide various utility functions.

Utility modules

npdf	NumpyDataFrame.
region
sequence_design

Networkx utilities

Specialized networkx algorithms for path and cycle finding.

algorithsm
exceptions
shortest_path
utils

Functions

bisect_between
bisect_slice_between
perfect_subject
prep_df
sort_with_keys

dasi.utils.bisect_between(a, low, high)

Returns the start (inclusive) and end (exclusive) indices for a sorted array using a key function.

Parameters

• a (Iterable) – sorted array (does not check)

• low (Any) – low key

• high (Any) – high key

Return type

Tuple[int, int]

Returns

tuple of start (inclusive) and end (exclusive) indices

dasi.utils.bisect_slice_between(a, keys, low, high)

Slice the iterable using inclusive bisection. Assumes both the iterable and keys are sorted. Bisect at specified low and high.

Parameters

• a (Iterable) – pre-sorted iterable to slice

• keys (Iterable) – pre-sorted keys to bisect

• low (Any) – low key

• high (Any) – high key

Return type

Iterable

Returns

sliced iterable

dasi.utils.group_by(arr, key)

Group a list by some key.

dasi.utils.log_metadata(key=None, class_attribute='_method_trace', additional_metadata=None)

wrapper for logging method run times for a class.

dasi.utils.log_times(key=None, class_attribute='_method_trace')

wrapper for logging method run times for a class.

dasi.utils.perfect_subject(data)

Determine whether a blast result consumes the entire subject.

dasi.utils.sort_with_keys(a, key)

Sort an iterable, returning both the sorted array and the sorted keys.

Parameters

• a (Iterable[Any]) – the iterable

• key (Callable) – key function to use for sorting

Return type

Tuple[List, List]

Returns