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

# <h1><span style="color:gray">ipyrad-analysis toolkit: </span> Astral species trees</h1>

# Once you've run treeslider you now have a distribution of gene trees that you can use as input to a multi-locu species tree or network inference program. Here I demonstrate how to input your data to **astral**.

# ### Required software

# In[1]:


# conda install ipyrad -c bioconda
# conda install toytree -c eaton-lab


# In[2]:


import pandas as pd
import toytree


# ### Short Tutorial:
# 
# 

# In[4]:


# load the tree table from CSV
tree_table = pd.read_csv(
    "./analysis-treeslider/test.tree_table.csv",
    index_col=0,
)


# In[59]:


# examine top of table
tree_table.head()


# ### Write the trees column to a file
# 

# In[11]:


outfile = open("trees.nwk", "w")
outfile.write("\n".join(tree_table.tree.tolist()))
outfile.close()


# ### Get Astral
# The following command will download and unzip Astral into the current directory. A binary to call the program *astral* will be located in the Astral directory. 

# In[12]:


get_ipython().run_cell_magic('bash', '', 'wget -q https://github.com/smirarab/ASTRAL/raw/master/Astral.5.6.3.zip \nunzip -qo Astral.5.6.3\n')


# ### Run Astral
# This will write the results (stdout) to a file called astral.tre, and it will write other information printed to the screen (stderr) to a file called astral.err. By default astral runs 100 bootstrap replicates by gene-tree resampling. To turn on gene and site resampling would require inputting the bootstrap files, which we did not currently save (we could...). 

# In[13]:


get_ipython().run_cell_magic('bash', '', 'java -jar Astral/astral.5.6.3.jar -i trees.nwk > astral.tre 2>astral.err\n')


# ### Plot astral species tree

# In[61]:


tre = toytree.rtree.coaltree(10)
tre.


# In[71]:


tre.rotate_node(names=["r0", "r1", "r2"])


# In[68]:


tre.draw(node_labels=True);


# In[60]:


tre = toytree.tree("astral.tre").root('reference')
tre.draw(node_labels="support", tip_labels_align=True);


# ### Plot astral species tree with quartet supports
# Not yet supported in toytree, what a wonky file format...