trviz.decomposer
Module Contents
Classes
- class trviz.decomposer.Decomposer(mode='DP')
- decompose(sequence, motifs, **kwargs)
Decompose sequence into motifs :param sequence: a string of tandem repeat sequence :param motifs: a set of motifs to be used for decomposition :param kwargs: keyword arguments for decomposer :return: decomposed sequence
- static _decompose_dp(sequence, motifs, **kwargs) List
Decompose sequence into motifs using dynamic programming
- Parameters
sequence – a string of VNTR sequence
motifs – a list of motif strings composed of nucleotide strings
**kwargs –
valid keywords are the following: match_score: a score for match mismatch_score: a score for mismatch min_score_threshold: a minimum score of the alignment.
- Returns
A list of decomposed motifs
- static _build_repeat_finder_hmm(motif, copies=1, has_flanking_sequence=False)
- _decompose_hmm(sequence, consensus_motif, **kwargs)
Decompose sequence into motifs using a HMM :param sequence: a string of VNTR sequence :param consensus_motif: A motif sequence :param **kwargs:
repeat_count: If not specified, use estimated repeat count based on the sequence and motif length
has_flanking_sequence: If true, use additional nodes in the HMM to identify flanking regions
verbose
- Returns
A list of decomposed motifs