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

# # Some sourmash command line examples!
# 
# [sourmash](https://sourmash.readthedocs.io/en/latest/) is research software from the Lab for Data Intensive Biology at UC Davis. It implements MinHash and modulo hash.
# 
# Below are some examples of using sourmash. They are computed in a Jupyter Notebook so you can run them yourself if you like!
# 
# Sourmash works on *signature files*, which are just saved collections of hashes.
# 
# Let's try it out!
# 
# ### Running this notebook.
# 
# You can run this notebook interactively via mybinder; click on this button:
# [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/dib-lab/sourmash/master?filepath=doc%2Fsourmash-examples.ipynb)
# 
# A rendered version of this notebook is available at [sourmash.readthedocs.io](https://sourmash.readthedocs.io) under "Tutorials and notebooks".
# 
# You can also get this notebook from the [doc/ subdirectory of the sourmash github repository](https://github.com/dib-lab/sourmash/tree/master/doc). See [binder/environment.yaml](https://github.com/dib-lab/sourmash/blob/master/binder/environment.yml) for installation dependencies.
# 
# ### What is this?
# 
# This is a Jupyter Notebook using Python 3. If you are running this via [binder](https://mybinder.org), you can use Shift-ENTER to run cells, and double click on code cells to edit them.
# 
# Contact: C. Titus Brown, ctbrown@ucdavis.edu. Please [file issues on GitHub](https://github.com/dib-lab/sourmash/issues/) if you have any questions or comments!

# ## Compute scaled signatures

# In[1]:


get_ipython().system('rm -f *.sig')
get_ipython().system('sourmash compute -k 21,31,51 --scaled=1000 genomes/*.fa --name-from-first -f')


# This outputs three signature files, each containing three signatures (one calculated at k=21, one at k=31, and one at k=51).

# In[2]:


ls *.sig


# We can now use these signature files for various comparisons.

# ## Search multiple signatures with a query
# 
# The below command queries all of the signature files in the directory with the `shew_os223` signature and finds the best Jaccard similarity:

# In[3]:


get_ipython().system('sourmash search -k 31 shew_os223.fa.sig *.sig')


# The below command uses Jaccard containment instead of Jaccard similarity:

# In[4]:


get_ipython().system('sourmash search -k 31 shew_os223.fa.sig *.sig --containment')


# ## Performing all-by-all queries
# 
# We can also compare all three signatures:

# In[5]:


get_ipython().system('sourmash compare -k 31 *.sig')


# ...and produce a similarity matrix that we can use for plotting:

# In[6]:


get_ipython().system('sourmash compare -k 31 *.sig -o genome_compare.mat')


# In[7]:


get_ipython().system('sourmash plot genome_compare.mat')

from IPython.display import Image
Image(filename='genome_compare.mat.matrix.png') 


# and for the R aficionados, you can output a CSV version of the matrix:

# In[8]:


get_ipython().system('sourmash compare -k 31 *.sig --csv genome_compare.csv')


# In[9]:


get_ipython().system('cat genome_compare.csv')


# This is now a file that you can load into R and examine - see [our documentation](https://sourmash.readthedocs.io/en/latest/other-languages.html) on that.

# ## working with metagenomes
# 
# Let's make a fake metagenome:

# In[10]:


get_ipython().system('cat genomes/*.fa > fake-metagenome.fa')
get_ipython().system('sourmash compute -k 31 --scaled=1000 fake-metagenome.fa')


# We can use the `sourmash gather` command to see what's in it:

# In[11]:


get_ipython().system('sourmash gather fake-metagenome.fa.sig shew*.sig akker*.sig')


# ## Other pointers
# 
# [Sourmash: a practical guide](https://sourmash.readthedocs.io/en/latest/using-sourmash-a-guide.html)
# 
# [Classifying signatures taxonomically](https://sourmash.readthedocs.io/en/latest/classifying-signatures.html)
# 
# [Pre-built search databases](https://sourmash.readthedocs.io/en/latest/databases.html)
# 
# ## A full list of notebooks
# 
# [An introduction to k-mers for genome comparison and analysis](kmers-and-minhash.ipynb)
# 
# [Some sourmash command line examples!](sourmash-examples.ipynb)
# 
# [Working with private collections of signatures.](sourmash-collections.ipynb)
# 
# [Using the LCA_Database API.](using-LCA-database-API.ipynb)
# 
# 
# 

# In[ ]: