workDir = '/home/nick/notebook/SIPSim/dev/fullCyc_trim/'

emp_data = 'SIP-core_unk_trm'
emp_data_preFrac = 'bulk-core_trm'

"""
Explanation: Description

Calculating summary tables (eg., shannon index) on trimmed fullCyc 12C-con dataset
These tables can be used for regression/correlation analysis against simulation data

Setting variables
End of explanation
"""


import os
import sys
%load_ext rpy2.ipython
%load_ext pushnote

if not os.path.isdir(workDir):
    os.makedirs(workDir)
    
%cd $workDir

"""
Explanation: Init
End of explanation
"""


!/home/nick/notebook/SIPSim/lib/R/shannon_calc.r -l \
    $emp_data > SIP-core_unk_shan.txt

!echo; head SIP-core_unk_shan.txt

"""
Explanation: Making a table of shannon index for each fraction community
End of explanation
"""


!/home/nick/notebook/SIPSim/lib/R/BD_span_calc.r -l \
    $emp_data $emp_data_preFrac > SIP-core_unk_trm_BD-span.txt

!echo; head SIP-core_unk_trm_BD-span.txt

"""
Explanation: Making a table of variance in BD spans

binning pre-fractionation abundances
calculating variance of BD span in each bin
End of explanation
"""


!/home/nick/notebook/SIPSim/lib/R/correlogram_make.r -l \
    $emp_data > SIP-core_unk_trm_corr.txt

!echo; head SIP-core_unk_trm_corr.txt

"""
Explanation: Making a community ~ BD correlogram
End of explanation
"""


