snp-dists_phylip.py

import sys
from io import StringIO

import pandas
from Bio.Phylo.TreeConstruction import DistanceMatrix


def distance_matrix(snp_tab):
    df = pandas.read_csv(snp_tab, sep='\t', header=0)
    cols = list(df.columns)[1:]

    matrix = [[int(f) for f in df[c].values][: i + 1] for i, c in enumerate(cols)]
    distmat = DistanceMatrix(cols, matrix=matrix)

    phylip = StringIO()
    distmat.format_phylip(phylip)
    print(phylip.getvalue())


distance_matrix(sys.stdin)