Analyzing the output
********************

sfs_code stores a great deal of information about each mutation or substitution
in a simulation, which can make it challenging to parse the output.  With
sfs_coder, all the data is stored internally in the Mutation class, allowing
for flexible manipulation of the output.

Opening and reading an output file
==================================

Opening and reading files is simple.  Below is an example that reads in all
the data in an SFS_CODE output file and calculates :math:`\pi` (the average 
pairwise diversity) in the 0th locus in all sampled populations.

.. code-block:: python

   from sfscoder import sfs
   import sys

   # an sfs_code output file that we will analyze
   f =sys.argv[1]

   # initializing a data object and setting the file path
   data = sfs.SFSData(file=f)

   # getting all the data from the simulations in the file
   data.get_sims()

   # The simulations in the file are stored in the data.sims attribute
   # for each Simulation object in data.sims, we can calculate pi for
   # a set of loci

   for sim in data.sims:
      
       pis = sim.calc_pi(loci=[0]) # array of pi values, indexed by population
       print pis[0]                # pis[0] is pi in the 0th population