Boundary Aligner¶
- pytadbit.boundary_aligner.aligner.align(sequences, method='reciprocal', **kwargs)[source]¶
Align Topologically Associating Domain borders. Supports multiple-alignment by building a consensus TAD sequence and aligning each experiment to it.
Note
as long as we are using multiple alignments in an iterative way, the order of sequences will be relevant. Here experiments are sorted according to the value of the first boundary found in order to try to reduce this problem.
- Parameters
method (reciprocal) – method used to align
- Returns
the result of the aligner used
- pytadbit.boundary_aligner.reciprocally.reciprocal(tads1, tads2, penalty=None, verbose=False, max_dist=100000)[source]¶
Method based on reciprocal closest boundaries (bd). bd1 will be aligned with bd2 (closest boundary from bd1) if and only if bd1 is the closest boundary of bd2 too (and of course if the distance between bd1 and bd2 is lower than max_dist).
- Parameters
tads1 – list of boundaries
tads2 – list of boundaries
penalty (None) – if None, penalty will be two times max_dist
verbose – print alignment
max_dist (100000) – distance threshold from which two boundaries can not be aligned together
- Returns
the alignment and a score between 0 and 1 (0: bad, 1: good).
- pytadbit.boundary_aligner.globally.needleman_wunsch(tads1, tads2, penalty=- 6.0, ext_pen=- 5.6, max_dist=500000, verbose=False)[source]¶
Align two lists of TAD boundaries using a Needleman-Wunsh implementation
- Parameters
tads1 – list of boundaries for one chromosome under one condition
tads2 – list of boundaries for the same chromosome under other conditions
penalty (-0.1) – penalty to open a gap in the alignment of boundaries
max_dist (500000) – distance from which match are denied. A bin_size of 20Kb the number of bins corresponding to 0.5Mb is 25
verbose (False) – print the Needleman-Wunsch score matrix, and the alignment of boundaries
- Returns
the max score in the Needleman-Wunsch score matrix.
