import sys
filename=sys.argv[1]
model=sys.argv[2]
numb=sys.argv[3]

from Bio import Phylo, AlignIO
from Bio.Phylo.TreeConstruction import DistanceCalculator, DistanceTreeConstructor
align = AlignIO.read(filename,'fasta')

comalign=align[:,0:1]

for j in range(align.get_alignment_length()):
  flag=0
  for i in align[:,j:(j+1)]:
    if i.seq == "-":
      flag=1
      break
  if flag == 0:
    comalign=comalign+align[:,j:(j+1)]

comalign=comalign[:,1:]
AlignIO.write(comalign, filename+".complete.phylip", "phylip")
calculator = DistanceCalculator(model)
distMatrix = calculator.get_distance(comalign)

constructor = DistanceTreeConstructor()
UPGMATree = constructor.upgma(distMatrix)
Phylo.draw_ascii(UPGMATree)
#Phylo.draw(UPGMATree)

import matplotlib
import matplotlib.pyplot as plt
from Bio import Phylo
from io import StringIO

def plot_tree(tree, output_file):
    matplotlib.rc('font', size=6)
    # set the size of the figure
    fig = plt.figure(figsize=(10, 20), dpi=100)
    # alternatively
    # fig.set_size_inches(10, 20)
    axes = fig.add_subplot(1, 1, 1)
    Phylo.draw(tree, axes=axes)
    plt.savefig(output_file, dpi=100)
    return

print("bootstrap: "+numb)
from Bio.Phylo.Consensus import *

calculator = DistanceCalculator(model)
constructor = DistanceTreeConstructor(calculator,'upgma')
trees = bootstrap_trees(comalign, int(numb), constructor)
tree = list (trees)
support_tree = get_support(UPGMATree, tree)
#Phylo.draw(support_tree)

for node in support_tree.get_nonterminals():
    node.name = None

plot_tree(support_tree, filename+".png")