changeo.Distance
Distance calculations
- changeo.Distance.calcDistances(sequences, n, dist_mat, sym='avg', norm=None)
Calculate pairwise distances between input sequences
- Parameters:
sequences – List of sequences for which to calculate pairwise distances
n – Length of n-mers to be used in calculating distance
dist_mat – pandas.DataFrame of mutation distances
norm – Normalization method. One of None, ‘len’, or ‘mut’.
sym – Symmetry method; one of ‘avg’ of ‘min.
- Returns:
numpy matrix of pairwise distances between input sequences
- Return type:
ndarray
- changeo.Distance.formClusters(dists, link, distance)
Form clusters based on hierarchical clustering of input distance matrix with linkage type and cutoff distance
- Parameters:
dists – numpy matrix of distances
link – Linkage type for hierarchical clustering
distance – Distance at which to cut into clusters
- Returns:
List of cluster assignments
- Return type:
- changeo.Distance.getAADistMatrix(mat=None, mask_dist=0, gap_dist=0)
Generates an amino acid distance matrix
- Parameters:
mat – Input distance matrix to extend to full alphabet; if unspecified, creates Hamming distance matrix that incorporates IUPAC equivalencies
mask_dict – Score for all matches against an X character
gap_dist – Score for all matches against a gap (-, .) character
- Returns:
pandas.DataFrame of distances
- Return type:
DataFrame
- changeo.Distance.getDNADistMatrix(mat=None, mask_dist=0, gap_dist=0)
Generates a DNA distance matrix
- Parameters:
mat – Input distance matrix to extend to full alphabet; if unspecified, creates Hamming distance matrix that incorporates IUPAC equivalencies
mask_dist – Distance for all matches against an N character
gap_dist – Distance for all matches against a gap (-, .) character
- Returns:
pandas.DataFrame of distances
- Return type:
DataFrame
- changeo.Distance.getNmers(sequences, n)
Breaks input sequences down into n-mers
- Parameters:
sequences – List of sequences to be broken into n-mers
n – Length of n-mers to return
- Returns:
Dictionary mapping sequence to a list of n-mers
- Return type:
- changeo.Distance.zip_equal(*iterables)
Zips iterables and raises exception if different lengths
- Parameters:
iterables – pointer to iterables to zip together
- Returns:
A generator of tuples with combined elements from the iterables
- Return type:
iter