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

# In[1]:


from qiime.plugins import phylogeny, alignment
from q2_types import  FeatureData, AlignedSequence, Sequence
import qiime

aligned_seqs = qiime.Artifact.import_data(FeatureData[AlignedSequence], 'aligned-dna-sequences.fasta')

# standard error goes to terminal where "jupyter notebook" is running
tree = phylogeny.methods.fasttree(aligned_seqs)
print(tree.tree.uuid)


# In[2]:


import sys
print("Hello world!!", file=sys.stderr)


# In[3]:


unaligned_seqs = qiime.Artifact.import_data(FeatureData[Sequence], 'dna-sequences.fasta')

# standard error goes to terminal where "jupyter notebook" is running
aln = alignment.methods.mafft(unaligned_seqs)
print(aln.alignment.uuid)


# In[4]:


sys.stderr.write('Hello world!')


# In[5]:


get_ipython().system('echo "testing" > /dev/stderr')


# In[6]:


# for the sake of completeness
get_ipython().system('cat aligned-dna-sequences.fasta')


# In[7]:


# for the sake of completeness
get_ipython().system('cat dna-sequences.fasta')


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