seqgra.model.data.sequenceelement module¶

MIT - CSAIL - Gifford Lab - seqgra

SequenceElement class definition, markup language agnostic

@author: Konstantin Krismer

class KmerBasedSequenceElement(sid: str, kmers: List[seqgra.schema.ProbabilisticToken])[source]¶

Bases: seqgra.model.data.sequenceelement.SequenceElement

generate() → str[source]¶

static get_by_id(sequence_elements: List[seqgra.model.data.sequenceelement.SequenceElement], sid: str) → seqgra.model.data.sequenceelement.SequenceElement ¶

get_max_length() → int[source]¶

normalize_probabilities() → None[source]¶

class MatrixBasedSequenceElement(sid: str, positions: List[List[seqgra.schema.ProbabilisticToken]])[source]¶

Bases: seqgra.model.data.sequenceelement.SequenceElement

generate() → str[source]¶

static get_by_id(sequence_elements: List[seqgra.model.data.sequenceelement.SequenceElement], sid: str) → seqgra.model.data.sequenceelement.SequenceElement ¶

get_max_length() → int[source]¶

normalize_probabilities() → None[source]¶

class SequenceElement(sid: str)[source]¶

Bases: abc.ABC

abstract generate() → str[source]¶

static get_by_id(sequence_elements: List[seqgra.model.data.sequenceelement.SequenceElement], sid: str) → seqgra.model.data.sequenceelement.SequenceElement [source]¶

abstract get_max_length() → int[source]¶

abstract normalize_probabilities() → None[source]¶