High Level Functions

pyrefinebio.high_level_functions.create_token(agree_to_terms=None, save_token=None)

Automatically creates a Token, activates it, and stores it to the Config file.

By default, will prompt the user before activating and storing the created Token.

Returns:

Token

Parameters:

  • agree_to_terms (bool) – if true, the token will be automatically activated without prompting. If false, the token will not be activated. Leave as None to be prompted before activating.

  • save_token (bool) – if true, the token will be automatically saved. If false, the token will not be saved. Leave as None to be prompted before saving.

pyrefinebio.high_level_functions.download_compendium(path, organism, version=None, quant_sf_only=False, extract=False, prompt=True)

Download a Compendium for the specified organism.

Returns:

Compendium

Parameters:

  • path (str) – the path that the Compendium should be downloaded to

  • organism (str) – the name of the Organism for the Compendium you want to download

  • version (int) – the version for the Compendium you want to download - None for latest version

  • quant_sf_only (bool) – true for RNA-seq Sample Compendium results or False for quantile normalized

  • extract (bool) – if true, the downloaded zip file will be automatically extracted

  • prompt (bool) – if true, will prompt before downloading files bigger than 1GB

pyrefinebio.high_level_functions.download_dataset(path, email_address, dataset_dict=None, experiments=None, aggregation='EXPERIMENT', transformation='NONE', skip_quantile_normalization=False, quant_sf_only=False, timeout=None, extract=False, prompt=True, notify_me=False)

Automatically constructs a Dataset, processes it, waits for it to finish processing, then downloads it to the path specified.

Returns:

Dataset

Parameters:

  • path (str) – the path that the Dataset should be downloaded to

  • email_address (str) – the email address that will be contacted with info related to the dataset

  • dataset_dict (dict) –

    a fully formed Dataset data attribute in the form: {

    ”Experiment”: [

    “Sample”, “Sample”

    ]

    } use this parameter if you want to specify specific Samples for your dataset each part of the dict can be a pyrefinebio object or an accession code as a string

  • experiments (list) – a list of Experiments that should be added to the dataset use this parameter if you only care about the Experiments - all available samples related to each Experiment will be added the list can contain Experiment objects or accession codes as strings

  • aggregation (str) – how the Dataset should be aggregated - by EXPERIMENT, by SPECIES, or by ALL

  • transformation (str) – the transformation for the dataset - NONE, MINMAX, or STANDARD

  • skip_quantile_normalization (bool) – control whether or not the dataset should skip quantile normalization for RNA-seq Samples

  • quant_sf_only (bool) – include only quant.sf files in the generated dataset.

  • timeout (datetime.timedelta) – if specified the function will return None after timeout is reached.

  • extract (bool) – if true, the downloaded zip file will be automatically extracted

  • prompt (bool) – if true, will prompt before downloading files bigger than 1GB

  • notify_me (bool) – if true, refine.bio will send you an email when the dataset has finished processing. Defaults to False.

pyrefinebio.high_level_functions.download_quantfile_compendium(path, organism, version=None, extract=False, prompt=True)

Download a Compendium for the specified organism. This function will always download RNA-seq Sample Compedium results.

Returns:

Compendium

Parameters:

  • path (str) – the path that the Compendium should be downloaded to

  • organism (str) – the name of the Organism for the Compendium you want to download

  • version (int) – the version for the Compendium you want to download - None for latest version

  • extract (bool) – if true, the downloaded zip file will be automatically extracted

  • prompt (bool) – if true, will prompt before downloading files bigger than 1GB

pyrefinebio.high_level_functions.help(entity=None)

Help

Prints out information about pyrefinebio’s classes and functions. To get information about a class method, pass in the class name and method name separated by either a space or a .

Examples

getting information about classes:

>>> pyrefinebio.help("Sample")

getting information about class methods:

>>> pyrefinebio.help("Sample.get")
or
>>> pyrefinebio.help("Sample get")

getting information about functions:

>>> pyrefinebio.help("download_dataset")