Map class¶
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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.
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__weakref__
¶ list of weak references to the object (if defined)
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add_alignment
(aln)[source]¶ Adds an Alignment object to the list of alignments
- Parameters
aln (Alignment) – Alignment to add
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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
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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
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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
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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
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