Sample

dbgen.tables.sample

class dbgen.tables.sample.RawFile(*args, **kwargs)
class dbgen.tables.sample.Sample(*args, **values)
Parameters
  • project – project code (e.g. ENA project)

  • run_accession – accession number

  • download_urls – list of URLs to download genome data

  • raw_data – file path to raw files (downloaded genome data)

  • cooked_data – list of references to results generated by bioinformatics tools

  • phenotypes – list of references to phenotypes

  • dataset – reference to sample dataset

  • species – reference to sample species

exception DoesNotExist
exception MultipleObjectsReturned
static download_raw_data(species_name: str = None, dataset_name: str = None)

Download raw data

Parameters
  • species_name – name of the species

  • dataset_name – name of the dataset

static save_result(sample_id: str, tool: str, version: str, date: str, parameters: str, raw_result_path: str)

Save the output results of a bioinformatic tool

Parameters
  • sample_id – sample ID

  • tool – bioinformatic tool name

  • version – bioinformatic tool version

  • date – date when the results have been collected

  • parameters – bioinformatic tool parameters

  • raw_result_path – path to the local output file

dbgen.tables.sample.import_data(species_name: str, dataset_name: str, dataset_file: str)

Import dataset

Parameters
  • species_name – species name

  • dataset_name – dataset names (e.g. name of the corresponding publication)

  • dataset_file – input file path