Map class

class biscot.Map.Map(map_id, labels_1, labels_2, alignments=[])[source]
__init__(map_id, labels_1, labels_2, alignments=[])[source]

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

__str__()[source]

Return str(self).

__weakref__

list of weak references to the object (if defined)

add_alignment(aln)[source]

Adds an Alignment object to the list of alignments

Parameters

aln (Alignment) – Alignment to add

add_channel_1_label(label_position)[source]

Adds a label to the list of channel 1 labels

Parameters

label_position (int) – Position of the label on the map

add_channel_2_label(label_position)[source]

Adds a label to the list of channel 2 labels

Parameters

label_position (int) – Position of the label on the map

check_containment()[source]

Parses the list of alignments in search of alignments that could be contained into another one, i.e. reference_start_aln_1 < reference_start_aln_2 and reference_end_aln_1 > reference_end_aln_2

Returns

List of tuples containing the contained alignment at the second position and the alignment containing it at the first position

Return type

list(tuple(Alignment, Alignment))

get_label_position(label_id, channel)[source]

Returns a label position on a map based on its id and channel

Parameters
  • label_id (integer) – Label id to look for

  • channel (int) – Enzyme channel of the searched label

Raises

Exception – If the label couldn’t be found

Returns

Searched label position

Return type

int

print_alignments()[source]

Prints the alignments of a Map object

sort_alignments()[source]

Sorts the list of alignments