Python Library Release Notes¶

Version 1.3.0: May 30, 2020¶

Updated schema set to v1.3.
Added load_repertoire, write_repertoire, and validate_repertoire to airr.interface to read, write and validate Repertoire metadata, respectively.
Added repertoire_template to airr.interface which will return a complete repertoire object where all fields have null values.
Added validate_object to airr.schema that will validate a single repertoire object against the schema.
Extended the airr-tools commandline program to validate both rearrangement and repertoire files.

Fixed a bug in the python reference library causing start coordinate values to be empty in some cases when writing data.

Updated schema set to v1.2.
Several improvements to the validate_rearrangement function.
Changed behavior of all airr.interface functions to accept a file path (string) to a single Rearrangement TSV, instead of requiring a file handle as input.
Added base argument to RearrangementReader and RearrangementWriter to support optional conversion of 1-based closed intervals in the TSV to python-style 0-based half-open intervals. Defaults to conversion.
Added the custom exception ValidationError for handling validation checks.
Added the validate argument to RearrangementReader which will raise a ValidationError exception when reading files with missing required fields or invalid values for known field types.
Added validate argument to all type conversion methods in Schema, which will now raise a ValidationError exception for value that cannot be converted when set to True. When set False (default), the previous behavior of assigning None as the converted value is retained.
Added validate_header and validate_row methods to Schema and removed validations methods from RearrangementReader.
Removed automatic closure of file handle upon reaching the iterator end in RearrangementReader.

Initial release.