src.data.common

Created on Fri Apr 30 15:13:32 2021

@author: Paolo Cozzi <paolo.cozzi@ibba.cnr.it>

Common stuff for smarter scripts

class src.data.common.AssemblyConf(version, imported_from)

Bases: tuple

imported_from

Alias for field number 1

version

Alias for field number 0

src.data.common.deal_with_datasets(src_dataset: str, dst_dataset: str, datafile: str) → [<class 'src.features.smarterdb.Dataset'>, <class 'src.features.smarterdb.Dataset'>, <class 'pathlib.Path'>]

Check source and destination dataset with its content

src.data.common.deal_with_sex_and_alias(sex_column: str, alias_column: str, row: Series)

Deal with sex and alias parameters

Parameters

• sex_column (str) – The sex column label.

• alias_column (str) – The alias column label.

• row (Series) – A row of metadata file.

Returns

• sex (SEX) – A SEX instance.

• alias (str) – The alias read from metadata table could be None.

src.data.common.fetch_and_check_dataset(archive: str, contents: list[str]) → [<class 'src.features.smarterdb.Dataset'>, list[pathlib.Path]]

Common operations on dataset: fetch a dataset by file (submitted archive), check that working dir exists and required file contents is in dataset. Test and get full path of required files

Parameters

• archive (str) – the dataset archive (file)

• contents (list) – a list of files which beed to be defined in dataset

Returns

a dataset instance list[Path]: a list of Path of required files

Return type

Dataset

src.data.common.get_sample_species(species: str) → Union[SampleSheep, SampleGoat]

Get a species name in input. It return the proper SampleSpecies class

Parameters

species (str) – the species name

Returns

a SampleSpecies class

Return type

Union[SampleSheep, SampleGoat]

src.data.common.get_variant_species(species: str) → Union[VariantSheep, VariantGoat]

Get a species name in input. It return the proper VariantSpecies class

Parameters

species (str) – the species name

Returns

a VariantSpecies class

Return type

Union[VariantSheep, VariantGoat]

src.data.common.new_variant(variant: Union[VariantSheep, VariantGoat], location: Location)

src.data.common.pandas_open(datapath: Path, **kwargs) → DataFrame

Open an excel or csv file with pandas and returns a dataframe

Parameters

• datapath (Path) – the path of the file

• kwargs (dict) – additional pandas options

Returns

file content as a pandas dataframe

Return type

pd.DataFrame

src.data.common.update_affymetrix_record(variant: Union[VariantSheep, VariantGoat], record: Union[VariantSheep, VariantGoat]) → [typing.Union[src.features.smarterdb.VariantSheep, src.features.smarterdb.VariantGoat], <class 'bool'>]

src.data.common.update_chip_name(variant: Union[VariantSheep, VariantGoat], record: Union[VariantSheep, VariantGoat]) → [typing.Union[src.features.smarterdb.VariantSheep, src.features.smarterdb.VariantGoat], <class 'bool'>]

src.data.common.update_location(location: Location, variant: Union[VariantSheep, VariantGoat], force_update: bool = False) → [typing.Union[src.features.smarterdb.VariantSheep, src.features.smarterdb.VariantGoat], <class 'bool'>]

Check provided Location with variant Locations: append new object or update a Location object if more recent than the data stored in database

Parameters

• location (Location) – The location to test against the database.

• variant (Union[VariantSheep, VariantGoat]) – The variant to test.

• force_update (bool, optional) – Force location update. The default is False.

Returns

A list with the updated VariantSpecie object and a boolean value which is True if the location was updated

Return type

[Union[VariantSheep, VariantGoat], bool]

src.data.common.update_probesets(variant_attr: list[src.features.smarterdb.Probeset], record_attr: list[src.features.smarterdb.Probeset]) → bool

Update probeset relying on object references

src.data.common.update_rs_id(variant: Union[VariantSheep, VariantGoat], record: Union[VariantSheep, VariantGoat]) → [typing.Union[src.features.smarterdb.VariantSheep, src.features.smarterdb.VariantGoat], <class 'bool'>]

src.data.common.update_sequence(variant: Union[VariantSheep, VariantGoat], record: Union[VariantSheep, VariantGoat]) → [typing.Union[src.features.smarterdb.VariantSheep, src.features.smarterdb.VariantGoat], <class 'bool'>]

src.data.common.update_variant(qs: QuerySet, variant: Union[VariantSheep, VariantGoat], location: Location) → bool

Update an existing variant (if necessary)