old_contents: #####################################################################
  # ~~~~~~~~~~~~~~~~~~
  # Tumor subtype and cell type independent DNA methylation alterations 
  # associated with stage progression in invasive breast carcinoma 
  # ~~~~~~~~~~~~~~~~~~
  # Way, G., Johnson, K., Christensen, B. 2015
  #
  # The custom python script will run the RefFree algorithm with 1000
  # bootstraps. The script will take about two days to complete the largest
  # data subset. It is possible to run on a personal machine but is not 
  # recommended. The analysis was performed on the DISCOVERY cluster computer
  # at Dartmouth College.
  #####################################################################
  
  import os
  import sys
  sys.path.insert(0, 'I.Data_Processing/Scripts/Functions')
  
  subtypes = ['Basal', 'Her2', 'LumA', 'LumB', 'Normal']
  stages = ['low', 'high']
  # bootstraps = 1000
  bootstraps = 1
  
  for i in subtypes:
  	for j in stages:
  		os.system('R --no-save --args '+bootstraps+' '+j+' '+i+' < II.RefFreeEWAS/Scripts/A.doRefFree2.R')
  
new_contents: #####################################################################
  # ~~~~~~~~~~~~~~~~~~
  # Tumor subtype and cell type independent DNA methylation alterations 
  # associated with stage progression in invasive breast carcinoma 
  # ~~~~~~~~~~~~~~~~~~
  # Way, G., Johnson, K., Christensen, B. 2015
  #
  # The custom python script will run the RefFree algorithm with 1000
  # bootstraps. The script will take about two days to complete the largest
  # data subset. It is possible to run on a personal machine but is not 
  # recommended. The analysis was performed on the DISCOVERY cluster computer
  # at Dartmouth College.
  #####################################################################
  
  import os
  import sys
  sys.path.insert(0, 'I.Data_Processing/Scripts/Functions')
  
  subtypes = ['Basal', 'Her2', 'LumA', 'LumB', 'Normal']
  stages = ['low', 'high']
  # bootstraps = 1000
  bootstraps = 1
  
  for i in subtypes:
  	for j in stages:
  		os.system('R --no-save --args '+str(bootstraps)+' '+str(j)+' '+str(i)+' < II.RefFreeEWAS/Scripts/A.doRefFree2.R')
  
subject: Fix string int concat