Sample

class pyrefinebio.Sample(id=None, title=None, accession_code=None, source_database=None, organism=None, platform_accession_code=None, platform_name=None, pretty_platform=None, technology=None, manufacturer=None, protocol_info=None, annotations=None, results=None, source_archive_url=None, has_raw=None, sex=None, age=None, specimen_part=None, genotype=None, disease=None, disease_stage=None, cell_line=None, treatment=None, race=None, subject=None, compound=None, time=None, is_processed=None, created_at=None, last_modified=None, contributed_metadata=None, contributed_keywords=None, original_files=[], computed_files=[], experiment_accession_codes=None, experiments=None)

Sample.

Retrieve a Sample based on accession code

>>> import pyrefinebio
>>> accession_code = "GSM000000"
>>> sample = pyrefinebio.Sample.get(accession_code)

Retrieve a list of Samples based on filters

>>> import pyrefinebio
>>> samples = pyrefinebio.Sample.search(is_processed=True, specimen_part="soft-tissue sarcoma")
classmethod get(accession_code)

Retrieve a Sample based on its accession code.

Returns:

Sample

Parameters:

accession_code (str) – The accession code for the Sample to be retrieved.

classmethod search(**kwargs)

Retrieve a list of Samples based on various filters

Returns:

list of Sample

Keyword Arguments:

  • ordering (str) – which field to use when ordering the results

  • title (str) – filter based on the Sample’s title

  • organism (str) – filter based on the Organism that the Sample was taken from

  • source_database (str) – filter based on the publically available repository that the Sample was taken from

  • source_archive_url (str) – filter based on Sample’s source url

  • has_raw (bool) – filter based on if the Sample had raw data available in the source database

  • platform_name (str) – filter based on the name of the Platform that was used to assay the Sample

  • technology (str) – filter based on the technology that was used to assay the Sample

  • manufacturer (str) – filter based on the manufacturer of the technology that was used to assay the Sample

  • sex (str) – filter based on the sex information provided by the submitter

  • age (number) – filter based on the age information provided by the submitter

  • specimen_part (str) – filter based on the part of the specimen reported by the submitter

  • genotype (str) – filter based on the genotype of the subject that the Sample was taken from

  • disease (str) – filter based on the disease information provided by the submitter

  • disease_stage (str) – filter based on the disease stage information provided by the submitter

  • cell_line (str) – filter based on the cell line used for the sample

  • treatment (str) – filter based on the treatment information provided by the submitter

  • race (str) – filter based on the race information provided by the submitter

  • subject (str) – filter based on the subject identifier information provided by the submitter

  • compound (str) – filter based on the compound information provided by the submitter

  • time (str) – filter based on the time information provided by the submitter

  • is_processed (bool) – filter based on if the Sample has been processed

  • is_public (bool) – filter based on if the Sample is public

  • limit (int) – number of results to return per page.

  • offset (int) – the initial index from which to return the results.

  • dataset_id (str) – filter based on the Dataset ids that the Sample has been added to

  • experiment_accession_code (str) – filter based on the Experiments that are associated with the Sample

  • accession_codes (str) – filter based on multiple accession codes at once