#!/usr/bin/env python3
# Usage: ./msa_approx.py score_matrix 5 test.fa
# Requires Alignment.py in the directory
from Alignment import Alignment
from Alignment import GetArguments
import sys
arguments = GetArguments(sys.argv)
test = Alignment(arguments.seqs, arguments.score_matrix, arguments.gapcost)
alignm = test.multiple_align()
for i in range(len(alignm)):
print(">", arguments.heads[test.seqOrder[i]])
print(test.num_to_sequence(alignm[i]), "\n")
