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
¶
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exception
MultipleObjectsReturned
¶
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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
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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