teemi.utils#

A script that provides utility functions

Functions

`counting_occurences`(data_with_occurences)	Count the occurences of each key in the input dict and returns the percentage of each key in the total values
`location_to_start_end_strand`(dictionary)	Convert "location" as Bio.SeqFeature.CompoundLocation to "start", "end", "strand" key-value pairs.
`mean`(lst)	Get mean from a list.
`multiply_list`(myList)	Multiplies elements one by one.
`nest_dict`(dictionary, key_for_nested_dict[, ...])
`remove_duplicates_with_name_attribute`(...)	Removes duplicate names from a list.
`remove_tuple_duplicates`(lst)	Removes tuple duplicates.
`rename_dict_keys`(dictionary, trans_dictionary)	Rename the keys of a dictionary using another dictionary.
`split_based_on_keys`(dictionary, key_list)	Split a dictionary into two based on a list of keys.
`start_end_to_location`(dictionary, length)	Start and End Key Value pair to Compound Location Key Value pair.
`unnest_dict`(dictionary, key_unnest_dict)	Unnest a dictionary by merging the values of a nested dictionary with the original dictionary, and renaming the key "label" to "name"

teemi.utils.counting_occurences(data_with_occurences: dict)[source]#

Count the occurences of each key in the input dict and returns the percentage of each key in the total values

Parameters:: data_with_occurences (dict) – The dictionary containing the data for counting occurences.
Returns:: A tuple containing two lists, the first one is the occurence percentage of each key, the second one is the list of keys.
Return type:: tuple

teemi.utils.location_to_start_end_strand(dictionary: Dict[str, Any]) → Dict[str, Any][source]#

Convert “location” as Bio.SeqFeature.CompoundLocation to “start”, “end”, “strand” key-value pairs.

Parameters:#

dictionaryDict[str, Any]: The input dictionary containing “location” key

Returns:#

dictionaryDict[str, Any]: The dictionary with “start”, “end”, “strand” key added and location removed.

teemi.utils.mean(lst: list)[source]#

Get mean from a list.

Parameters:: lst (list of floats.)
Returns:: mean
Return type:: float

teemi.utils.multiply_list(myList)[source]#

Multiplies elements one by one.

Parameters:: myList (list) – list of integers to be multiplied
Returns:: result
Return type:: int

teemi.utils.nest_dict(dictionary: Dict[Any, Any], key_for_nested_dict: str, first_order_keys: List[str] = None) → Dict[Any, Any][source]#

” Nest a dictionary by moving the values of specified keys to a nested dictionary.

Parameters:#

dictionaryDict[Any, Any]: The input dictionary
key_for_nested_dictstr: The key to use for the nested dictionary
first_order_keysList[str], optional: List of keys to keep in the first level of the dictionary, by default None

Returns:#

dictionaryDict[Any, Any]: The nested dictionary

teemi.utils.remove_duplicates_with_name_attribute(record_with_duplicates) → list[source]#

Removes duplicate names from a list.

Parameters:: record_with_duplicates (list) – list with duplicated elements
Returns:: recs_no_dup – list without duplicates
Return type:: list

teemi.utils.remove_tuple_duplicates(lst: list) → list[source]#

Removes tuple duplicates.

Parameters:: lst (list) – list with duplicated elements
Returns:: without duplicates
Return type:: list

teemi.utils.rename_dict_keys(dictionary: Dict, trans_dictionary: Dict) → Dict[source]#

Rename the keys of a dictionary using another dictionary.

Parameters:

dictionary (Dict[K, V]) – The input dictionary
trans_dictionary (Dict[K, K]) – The dictionary containing the keys to be replaced as keys and the new keys as values

Returns:

dictionary – The dictionary with the keys renamed.

Return type:

Dict[K, V]

teemi.utils.split_based_on_keys(dictionary: Dict[Any, Any], key_list: List[str]) → Tuple[Dict[Any, Any], Dict[Any, Any]][source]#

Split a dictionary into two based on a list of keys.

Parameters:

dictionary (Dict[Any, Any]) – The input dictionary
key_list (List[str]) – The list of keys to split the dictionary on

Returns:

first_dict (Dict[Any, Any]) – The dictionary containing the keys specified in key_list
other_dict (Dict[Any, Any]) – The dictionary containing the keys not specified in key_list

teemi.utils.start_end_to_location(dictionary: Dict[str, Any], length: int) → Dict[str, Any][source]#

Start and End Key Value pair to Compound Location Key Value pair.

Parameters:#

dictionaryDict[str, Any]: The input dictionary containing “start” and “end” keys
lengthint: The length of the sequence

Returns:#

dictionaryDict[str, Any]: The dictionary with “location” key added and start, end removed.

teemi.utils.unnest_dict(dictionary: Dict[Any, Any], key_unnest_dict: str) → Dict[Any, Any][source]#

Unnest a dictionary by merging the values of a nested dictionary with the original dictionary, and renaming the key “label” to “name”

Parameters:#

dictionaryDict[Any, Any]: The input dictionary
key_unnest_dictstr: The key of the nested dictionary to unnest

Returns:#

dictionaryDict[Any, Any]: The unnested dictionary