#!/usr/bin/env python
# coding: utf-8

# In[1]:


from __future__ import print_function
import os
import shutil

import dendropy
from dendropy.interop import raxml


# In[2]:


ebola_data = dendropy.DnaCharacterMatrix.get_from_path('trim.fasta', 'fasta')
rx = raxml.RaxmlRunner()
ebola_tree = rx.estimate_tree(ebola_data, ['-m', 'GTRGAMMA', '-N', '10'])
print('RAxML temporary directory: %s' % rx.working_dir_path)
del ebola_data


# In[3]:


ebola_tree.write_to_path('my_ebola.nex', 'nexus')


# In[4]:


import matplotlib.pyplot as plt
from Bio import Phylo
get_ipython().run_line_magic('matplotlib', 'inline')
my_ebola_tree = Phylo.read('my_ebola.nex', 'nexus')
my_ebola_tree.name = 'Our Ebolavirus tree'

fig = plt.figure(figsize=(16, 18))
ax = fig.add_subplot(1, 1, 1)
Phylo.draw(my_ebola_tree, axes=ax)


# ## RAxML with Biopython

# In[5]:


import random
import sys
from Bio.Phylo.Applications import RaxmlCommandline
raxml_cline = RaxmlCommandline(sequences='trim.fasta',
                               model='GTRGAMMA', name='biopython',
                               num_replicates='10',
                               parsimony_seed=random.randint(0, sys.maxint),
                               working_dir=os.getcwd() + os.sep + 'bp_rx')
print(raxml_cline)
try:
    os.mkdir('bp_rx')
except OSError:
    shutil.rmtree('bp_rx')
    os.mkdir('bp_rx')
out, err = raxml_cline()


# In[6]:


from Bio import Phylo
biopython_tree = Phylo.read('bp_rx/RAxML_bestTree.biopython', 'newick')


# In[7]:


print(biopython_tree)


# In[ ]: