Map-related methods

biscot.Map.check_map_containment(reference_maps_dict)[source]

Parses all alignments of a map in search of contaned alignments

Parameters

reference_maps_dict (dict(int: Map)) – Dict containing anchor maps

Returns

A list containing containing contained alignments

Return type

list(tuple(Alignment, Alignment))

biscot.Map.parse_contig_cmap(cmap_1_path, cmap_2_path)[source]

Parses one or two contig CMAP files to extract contig labels

Parameters
  • cmap_1_path (str) – Path to a CMAP file

  • cmap_2_path (str) – Path to a CMAP file

Returns

Dict containing contg maps

Return type

dict(str: Map)

biscot.Map.parse_reference_cmap(reference_cmap_file_path)[source]

Parses a reference CMAP file to extract anchor labels

Parameters

reference_cmap_file_path (str) – Path to a CMAP file

Returns

Dict containing anchor maps

Return type

dict(int, Map)

biscot.Map.sort_map_alignments(reference_maps_dict)[source]

Sorts the alignments of a Map object by reference_start value

Parameters

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