Generate ENVIRONMENT from VAMPS Matrix that was converted from BIOM format...

gen_ENVIRONMENT_from_VAMPS_matrix.py

import sys

matrix = open(sys.argv[1])
env = open(sys.argv[1] + '.ENV', 'w')

matrix.readline()
samples = matrix.readline().strip().split('\t')[1:]

for line in matrix.readlines():
    fields = line.strip().split('\t')
    taxon = fields[0].strip()
    counts = [int(float(x)) for x in fields[1:]]
    for i in range(0, len(counts)):
        if counts[i]:
            env.write('%s\t%s\t%d\n' % (taxon, samples[i], counts[i]))

env.close()