Created
November 22, 2017 08:56
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From newick to distance matrix
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| #!/usr/bin/env python | |
| if __name__ == "__main__": | |
| import sys | |
| if len(sys.argv) < 2: | |
| print('USAGE: python nwk2mat.py TREE.nwk') | |
| sys.exit(1) | |
| import pandas as pd | |
| import itertools | |
| from Bio import Phylo | |
| ifile = sys.argv[1] | |
| t = Phylo.read(ifile, 'newick') | |
| d = {} | |
| for x, y in itertools.combinations(t.get_terminals(), 2): | |
| v = t.distance(x, y) | |
| d[x.name] = d.get(x.name, {}) | |
| d[x.name][y.name] = v | |
| d[y.name] = d.get(y.name, {}) | |
| d[y.name][x.name] = v | |
| for x in t.get_terminals(): | |
| d[x.name][x.name] = 0 | |
| m = pd.DataFrame(d) | |
| m.to_csv(sys.stdout, sep='\t') |
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