convert 2d matrix to flat three column

convert_distance_matrix.py

### this script takes in a distance matrix produced by https://github.com/tseemann/nullarbor/blob/master/bin/afa-pairwise.pl which is a 2d matrix

#   a  b  c
# a 0  1  2
# b 1  0  1
# c 2  1  0

# and prints out the half matrix in three column format, with no self-self comparisons

# a b 1
# a c 2
# b c 1

## personally, i find this format a little easier to work with in iterating through all the pairs etc.

def read_in_matrix(infile):
	strains = []
	diff_matrix = {}
	with open(infile) as fi:
		lines = fi.readlines()
		# the first row is the header
		header = lines.pop(0)
		strains = header.strip().split('\t')
		## the first item in the header is 'ID', get rid of this.
		strains = strains[1:]
		for line in lines:
			split_line = line.split('\t')
			## first element in the split line is the strain id
			strain1 = split_line.pop(0)
			diff_matrix[strain1] = {}
			for i, strain2 in enumerate(strains):
				if strain2 in diff_matrix and strain1 not in diff_matrix[strain2]:
					diff_matrix[strain1][strain2] = split_line[i]
	return diff_matrix


def print_matrix(diff_matrix):
	for strain1 in diff_matrix:
		for strain2 in diff_matrix[strain1]:
			if strain1 != strain2:
				print '\t'.join([strain1, strain2, diff_matrix[strain1][strain2]])

def main():
  ## output of afa-pairwise.pl
	infile = 'data/2016.07.27/st4.dist'
	diff_matrix = read_in_matrix(infile)
	print_matrix(diff_matrix)

main()