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 nmers 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 nmers
 Parameters
sequences – List of sequences to be broken into nmers
n – Length of nmers to return
 Returns
Dictionary mapping sequence to a list of nmers
 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