rna_library.structure.parser

Module Contents

Functions

helix_length(connections, start)	TODO
get_junction_or_hairpin(sequence, connections, start)	TODO
get_helix(sequence, connections, start)	TODO
get_singlestrand(sequence, connections, start)	TODO
get_motifs(sequence, connections, start)	Helper method
parse_to_motifs(structure, sequence)	Method takes a structure sequence pair and returns a root Motif() with a complete associated graph.

rna_library.structure.parser.helix_length(connections, start)

TODO

Parameters

• connections (List[int]) –

• start (int) –

Return type

int

rna_library.structure.parser.get_junction_or_hairpin(sequence, connections, start)

TODO

Parameters

• sequence (str) –

• connections (List[int]) –

• start (int) –

Return type

Union[rna_library.structure.junction.Junction, rna_library.structure.hairpin.Hairpin]

rna_library.structure.parser.get_helix(sequence, connections, start)

TODO

Parameters

• sequence (str) –

• connections (List[int]) –

• start (int) –

Return type

Union[rna_library.structure.hairpin.Hairpin, rna_library.structure.helix.Helix, rna_library.structure.junction.Junction, rna_library.structure.singlestrand.SingleStrand]

rna_library.structure.parser.get_singlestrand(sequence, connections, start)

TODO

Parameters

• sequence (str) –

• connections (List[int]) –

• start (int) –

Return type

rna_library.structure.singlestrand.SingleStrand

rna_library.structure.parser.get_motifs(sequence, connections, start)

Helper method

Parameters

• sequence (str) –

• connections (List[int]) –

• start (int) –

Return type

Union[rna_library.structure.helix.Helix, rna_library.structure.singlestrand.SingleStrand]

rna_library.structure.parser.parse_to_motifs(structure, sequence)

Method takes a structure sequence pair and returns a root Motif() with a complete associated graph.

Parameters

• structure (str) – a valid dot-bracket structure

• sequence (str) – the corresponding sequence composed of the alphabet [ACGUTNB]

Returns

motif

Return type

Motif