--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Matrix_Validate_import.py	Tue Nov 27 14:20:40 2018 -0500
@@ -0,0 +1,179 @@
+'''
+Created on Jun 7, 2017 modified Feb2018
+
+@author: cjacoby and Bob Brown
+'''
+ 
+import sys, traceback, argparse
+import numpy as np
+import os
+#import matplotlib.pyplot as plt
+#import matplotlib.pyplot as plt; plt.rcdefaults()
+
+# Define the Reading Function Which Pulls the Data from a .txt file
+def reader(input_file_txt, create_plot= False):
+    #Read Matrix, Preserving String Values for Headers first row and first column (both minus first cell) 
+    #Read Matrix, Converting all values to Float for Data Processing    
+        
+    f = open(input_file_txt, "rU")
+
+    #print( 'Valid NAN identifiers are: empty cells, cells with blanks,"NA","N/A","-", and "?"')
+
+    column_labels = []
+    row_labels = []
+    matrix  = []
+    firstLine= True
+    
+    line = f.readline()
+
+#    "NA","N/A","-","?","NAN","NaN","Na","na","n/a","null",EMPTY/Null, SPACE (blank char) 
+
+    nanList    = ["", " ","NAN", "NA", "N/A", "-","?"]
+    binCatDict = {"":0, " ":0, "Text":0, "NA":0, "-":0,"NAN":0, "N/A":0,"?":0}
+    row       = 0
+    nanCnt    = 0
+    nonNumCnt = 0
+    
+    while line:
+        line = line.strip("\n")
+        line = line.split('\t')
+
+        row += 1
+        
+        if firstLine: 
+            lengthRow = len(line)
+            column_labels   = line[1:]
+        else:
+            if lengthRow != len(line):
+               # print("\nERROR matrix row lengths unequal for row 0 and row "+str(row)+"\n" )
+                sys.exit(-1)
+            
+            temp  = []
+#            column= 0
+            row_labels.append(str(line[0]))
+           
+            #for item in line[1:]:  use enumerate
+            for column, item in enumerate(line[1:],1):
+#                column += 1
+                try:
+                    temp.append(float(item))
+                except ValueError:
+                    temp.append(np.nan)
+                    itemUC= item.upper()
+                    
+                    if itemUC in nanList:
+                        nanCnt += 1
+                        binCatDict[itemUC]= binCatDict[itemUC]+1
+                       # print( 'Legit nans= ',str(item))
+                    else:
+                        if nonNumCnt == 0:  sys.stderr.write("Start List of up to first 50 Invalid cell values \n")
+                        nonNumCnt +=1
+                        if nonNumCnt < 50:  sys.stderr.write("At row_column= "+str(row)+"_"+str(column)+' invalid data cell value '+ item+"\n")
+                       
+            matrix.append(temp)
+            
+        line = f.readline()
+        firstLine= False
+                   
+    #sys.stdout.write("\n\n")
+    f.close()
+    binCatDict["Text"]= nonNumCnt
+
+# plot results of NAN counts above
+
+    binCat = ["null", "blank", 'hyphen', '?','NA','N/A' ,'NAN', 'text']
+    orderDict= {0:"", 1:"", 2:'-', 3:'?',4:'NA',  5:'N/A' ,6:'NAN', 7:'Text'}
+#TODO verify dict orde for data    
+        #print("> key value  =",key, str(value))
+
+    if create_plot:    
+        numBins = len(binCat)
+        binWidth = 1
+        bins     = []
+        binData  = []
+        
+        for key in sorted(orderDict):
+            value= binCatDict[orderDict[key]]   # place items on chart in order and with data value for item
+            if value < 1:
+                binData.append(value+0.01)
+            else:
+                binData.append(value)
+
+        #"""
+        for j in range(numBins):
+            bins.append(j*binWidth)
+    #ttps://pythonspot.com/matplotlib-bar-chart/
+        y_pos = np.arange(numBins)
+        plt.yticks(y_pos, binCat)
+        plt.title("Distribution of NAN types (UPPER & lower & MiXeD case combined)")
+        plt.ylabel('NAN Types')
+        plt.xlabel('Occurrences')
+        #plt.legend()
+        plt.barh(y_pos, binData, align='center', alpha=0.5)
+    
+        fig, ax = plt.subplots(num=1, figsize=(8,3))
+        ax.set_title("Data Cell Counts of Not A Number (NAN) Types")
+        #ax.bar(center,bins, align='center', width=width)
+        #ax.bar(center, hist, align='center', width=width)
+        #ax.set_xticks(bins)
+    #    fig.savefig("/Users/bobbrown/Desktop/Matrix-tools-Test-output/NAN-plot.png")
+        
+    #    fig, ax = plt.subplots(num=1, figsize=(8,3))
+    #    fig.savefig("/Users/bobbrown/Desktop/Matrix-tools-Test-output/hist-out.png")
+        
+        plt.show()
+        #"""
+
+#after plot error?
+    x,y=np.shape(matrix)
+    if nanCnt > 0: print("WARNING -- Found "+str(nanCnt)+" Valid Non-numbers. Their percent of total matrix data cell values = "+str((100*nanCnt)/(x*y))+"% ")
+    if nonNumCnt > 0:  sys.exit(-1)
+    #print ("reader output:")
+    #print (matrix)
+    #print (column_labels)
+    #print(row_labels)
+    return matrix,column_labels,row_labels
+
+#----------------------------------------------------------------------
+# Verify Matrix A  column_labels match Matrix B row_labels in name and order for A*B 
+def MatchLabels(column_labels,row_labels):
+     
+        if len(column_labels) != len(row_labels):
+            sys.err("ERROR 1st matrix column count "+str(len(column_labels))+" not equal 2nd Matrix number row count "+str(len(row_labels))+"\n" )
+        else:
+            cnt= 0
+            for k in range(0,len(column_labels)):
+                if column_labels[k] != row_labels[k] and cnt < 20:
+                    cnt += 1
+                    #sys.err("ERROR At column & row position "+str(k)+" Matrix 1 column value "+str(column_labels)+" not equal 2nd Matrix row value "+str(row_labels)+"\n" )
+            
+            if cnt > 0: 
+                sys.exit(-11)
+#----------------------------------------------------------------------
+# restores row and column labels in ouput
+def Labeler(matrix,column_labels,row_labels,output_file_txt):
+    #print("matrix length: " + str(len(matrix)))
+    #print("row labels length: " + str(len(row_labels)))
+    #print("col labels length: " +str(len(column_labels)))
+    #Define Null Sets For Col and Row Headers
+    with open(output_file_txt,'w') as f:
+        f.write("")
+        for k in range(0,len(column_labels)):
+                f.write('\t' + str(column_labels[k]) )
+        f.write('\n')
+        #for i in range(0,len(row_labels)):
+        for i in range(0,len(matrix)):
+                f.write(str(row_labels[i]) )
+                #print("matrix["+str(i)+"] length:" + str(len(matrix[i])))
+                for j in range(0,len(matrix[0])):
+                        f.write('\t' + format(matrix[i][j]))
+                f.write('\n')
+
+
+#----------------------------------------------------------------------
+if __name__ == '__main__':
+    input_file_txt = str(sys.argv[1])
+                                 
+    matrix,column_labels,row_labels = reader(input_file_txt)
+    print("Done")
+