Alignment class

class biscot.Alignment.Alignment(map_id, reference_id, map_start, map_end, reference_start, reference_end, channel, orientation, alignments)

__init__(map_id, reference_id, map_start, map_end, reference_start, reference_end, channel, orientation, alignments)

Initialize self. See help(type(self)) for accurate signature.

__str__()

Text representation of an Alignment object

Returns

String representing the Alignment object

Return type

str

__weakref__

list of weak references to the object (if defined)

get_corresponding_contig_map_label(reference_label_id)

Extracts a contig map label that was aligned against specified anchor label

Parameters

reference_label_id (int) – Anchor map label id

Returns

Contig map label id

Return type

int

update_alignments(contig_maps_dict)

Parses contig maps and removes alignment when aln.map_start < self.map_start or aln.map_end > self.map_end

Parameters

contig_maps_dict (dict(int, Map)) – Dict containing contig Map objects