Key file related methods

biscot.Key.extend_key_dict(key_dict, reference_maps_dict)[source]

Adds the reference id to the key_dict key as a contig can be placed multiple times and we don’t want to modify its key informations erroneously in case of contained alignments

Parameters
  • key_dict (dict((int, int), (str, int, int, int))) – Dict containing the correspondance between contigs and contig maps

  • reference_maps_dict (dict(int, Map)) – Dict containing reference anchor maps

Returns

Key dict containing the correspondance between contigs and contig maps, with the added information of reference id

Return type

dict((int, int, int), (str, int, int, int))

biscot.Key.get_max_id(key_dict)[source]

Gets the max id found inside a key_dict keys

Parameters

key_dict (dict((int, int, int), (str, int, int, int))) – Dict containing the correspondance between contigs and contig maps

Returns

Maximum value of the key_dict keys

Return type

int

biscot.Key.parse_key(key_file_path)[source]

Parses a Bionano ‘.key’ file and extracts informations about contigs and their contig map counterparts

Parameters

key_file_path (str) – Path to a ‘.key’ file

Returns

Dict containing the correspondance between contigs and contig maps

Return type

dict((id: int, channel: int), (contig_name: str, start: int, end:int, size: int))