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

# # Tutorial 6: CPTAC basics review
# 
# 
# First, we'll import the package.

# In[1]:


import cptac


# We can list which cancers we have data for.

# In[2]:


cptac.get_cancer_options()


# ## Load the BRCA dataset

# In[3]:


br = cptac.Brca()


# We can list which data types are available from which sources.

# In[4]:


br.list_data_sources()


# ## Download
# 
# Each file will be automatically downloaded when requested, but authentication through your Box account is required to download pancan data.
# 
# See the end of this tutorial for how to download files on a remote computer that doesn't have a web browser for logging into Box.

# Let's get some data tables.

# In[5]:


br.get_clinical(source="mssm")
#Note: the syntax above is optional, calling the function as br.get_clinical('mssm') works just as well


# In[6]:


br.get_somatic_mutation('harmonized')


# In[7]:


br.get_proteomics(source="umich")