--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/src/breadcrumbs/scripts/scriptEnvToTable.py	Tue May 13 21:58:57 2014 -0400
@@ -0,0 +1,56 @@
+#!/usr/bin/env python
+"""
+Author: Timothy Tickle
+Description: Convert Env file to table
+"""
+
+__author__ = "Timothy Tickle"
+__copyright__ = "Copyright 2012"
+__credits__ = ["Timothy Tickle"]
+__license__ = ""
+__version__ = ""
+__maintainer__ = "Timothy Tickle"
+__email__ = "ttickle@sph.harvard.edu"
+__status__ = "Development"
+
+import sys
+import argparse
+import csv
+
+
+#Set up arguments reader
+argp = argparse.ArgumentParser( prog = "scriptEnvToTable.py",
+    description = """Convert Env file to table""" )
+
+#Arguments
+#For table
+argp.add_argument("strEnvFile", metavar = "EnvFile", help ="EnvFile data file")
+argp.add_argument("strOutputFile", metavar = "OutputFile", help ="Output File")
+args = argp.parse_args( )
+
+hndlReader = csv.reader(open(args.strEnvFile,'rU'), delimiter="\t")
+
+lsListOfIDs = []
+lsListOfFeatures = []
+dictValues = {}
+for lsLine in hndlReader:
+  print(lsLine)
+  lsListOfIDs.append(lsLine[1])
+  lsListOfFeatures.append(lsLine[0])
+  tpleKey = tuple([lsLine[1],lsLine[0]])
+  if tpleKey in dictValues:
+    print("Error:: Duplicate key entries found")
+    exit(1)
+  dictValues[tpleKey] = lsLine[2]
+
+lsListOfIDs = list(set(lsListOfIDs))
+lsListOfFeatures = list(set(lsListOfFeatures))
+print(lsListOfIDs)
+print(lsListOfFeatures)
+hndlWrite = csv.writer(open(args.strOutputFile,'w'), delimiter="\t")
+hndlWrite.writerow(["ID"]+lsListOfIDs)
+for sFeature in lsListOfFeatures:
+  lsFeatureLine = [sFeature]
+  for sSample in lsListOfIDs:
+    lsFeatureLine.append(dictValues.get(tuple([sSample,sFeature]),0))
+  hndlWrite.writerow(lsFeatureLine)