samples_db creates and queries a database containing of familial statuses and mean coverage.

samples_db.create_db(trios_file, coverage_file, delete=False)

Creates a database containing trio information.

Parameters:

• trios_file (str) – The path to a file containing trio information.
• coverage_file (str) – The path to a file containing mean coverage for samples.
• delete (bool) – Flag that determines if the sqlite database file will be overriden when running this function.

Samples files are available in the sample_db_files directory from this repository.

samples_db.get_coverage_for_sample(s)

Executes a query over the datavase to find the coverage for a given sample.

Parameters:s (str) – The sample (e.g. LP6005057-DNA_F03) Returns:The mean coverage for this sample. Return type:str (could be casted to a float)

samples_db.get_sample_ids_for_family(f)

Executes a query over the database to find the samples from a given family.

Parameters:f (str) – The family (e.g. 1443) Returns:A dictionary containing the familial status (mother, father, twin1 or twin2 as a key and the sample id as a value.