--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mda_heatmap_gen.py	Thu Jul 20 15:31:06 2017 -0400
@@ -0,0 +1,250 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+# python shell program to validate ng-chm heat map input matrix file and covariate file formats before calling java shell -- bob brown
+
+import subprocess           #you must import subprocess so that python can talk to the command line
+import sys
+import os
+import re
+#import config
+import traceback
+#import commons
+
+#ConfigVals = config.Config("../rppaConf.txt")
+
+def main():
+    
+    try:
+        print '\nStarting Heat Map file validation ......' 
+        #print "\nheat map sys args len and values = ",len(sys.argv), str(sys.argv)   #, '++',argvals
+
+      
+        error= False
+        endCovarParam=  len(sys.argv)-2 # IF any ending of loc for covar triplet info 
+        startCovarParam=    17 # beginning loc for covar triplet info
+        inMatrix=           sys.argv[3]
+
+        for i in range( endCovarParam, 15, -3):
+            if len(sys.argv[i]) > 6:
+                if sys.argv[i][0:4].find('row_') == 0 or sys.argv[i][0:7].find('column_') == 0:  # 0 is match start position
+                    startCovarParam= i-2                
+                    #print "\nHeat map arg 3 and start covariate index on = " ,str(sys.argv[3]),' - ', startCovarParam, ' covar name= ',str(sys.argv[startCovarParam:])
+                #else: print '\nCovariate param row or column not found at i', i, str(sys.argv[i])
+
+    #test        inMatrix= "/Users/bobbrown/Desktop/NGCHM-Galaxy-Test-Files/400x400firstRowShift.txt"
+    #test        covarFN= '/Users/bobbrown/Desktop/400x400-column-covariate-continuous-TestingErrors.txt'
+    #test        row_col_cat_contin= 'column_continuous'
+    #test        row_col_cat_contin= 'column_categorical'  
+    #test        covarLabel = 'bob test'
+    #test        numCovariates= 1
+        
+        errorInMatrix,inMatrixRowLabels,inMatrixColLabels= ValidateHMInputMatrix(inMatrix)   # verify input matrix
+        
+        print "\nFirst & last Row labels ", inMatrixRowLabels[0],inMatrixRowLabels[-1]," and Columns ", inMatrixColLabels[0],inMatrixColLabels[-1], " number Rows= ",len(inMatrixRowLabels)," number Columns= ",len(inMatrixColLabels)
+            
+    # continue reviewing covariates to catch any errors in any of the input info
+        if len(inMatrixRowLabels) < 5 or len(inMatrixColLabels) < 5: 
+            errorInMatrix = True
+            print '\n----ERROR Input matrix has too few columns and rows need to ignore validating covariate files for now'
+            
+        elif not errorInMatrix: 
+            print "\n++++ SUCCESS the Input Matrix looks good\n\n"
+            
+            i= startCovarParam
+            while i < (len(sys.argv)-2):  # todo verify this works with advances tool is one other 0->n param after this
+                covarLabel=         sys.argv[i]
+                covarLabel=         covarLabel.replace(' ','')
+                covarFN=            sys.argv[i+1]
+                covarFN=            covarFN.replace(' ','')
+                row_col_cat_contin=  sys.argv[i+2]
+                row_col_cat_contin=  row_col_cat_contin.replace(' ','')
+                i +=3
+                                             
+                print "\nSTART Validating covariate file with label= ", covarLabel, " and type= ",row_col_cat_contin
+        
+                error= ValidateHMCorvarFile(covarLabel, covarFN, row_col_cat_contin,inMatrixRowLabels,inMatrixColLabels)  # check covariate files
+    
+            if error or errorInMatrix:
+                print"\n---ERROR issues found in input or covariate files\n "
+                sys.stderr.write( "\nERROR issues found in input or covariate files see errors in Standard Output\n\n ") 
+                sys.exit(3)
+            
+                
+        print"\n FINISHED -- Validation of the Input Matrix and Covariate files (if any)\n\n"
+        
+        #print" next running the clustered heat map generator \n",str(sys.argv[11])+"/heatmap.sh "+ str(sys.argv[1:])
+    #            p = subprocess.Popen([str(sys.argv[1])+"/heatmap.sh "+ argvals], shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
+            #p = subprocess.Popen([str(sys.argv[11])+"/heatmap.sh "+ str(sys.argv[1:])], shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
+     
+            #retval = p.wait()  
+            #print ' Cluster and Viewer returned\n'
+            #for line in p.stdout.readlines():
+            #    print line
+                     
+#         else: 
+#             sys.stderr.write("\nERROR -- The Heat Map Generator encountered the above errors with the input file(s)\n\n")
+#             sys.exit(3) # this will error it out :)
+#     except:
+#         sys.stderr.write(str(traceback.format_exc()))
+#         sys.exit(3) # this will error it out :)
+    except Exception, err:
+        sys.stderr.write('ERROR: %sn' % str(err))
+
+    return 
+
+#+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-
+
+def ValidateHMInputMatrix(inputMatrixPath):           # This sub routine ensures that the slide design input by the user matches a slide design on record
+
+     try:
+        error= True
+    
+        inputMatrixPath= inputMatrixPath.replace(' ','')
+
+        inMatrixFH= open( inputMatrixPath, 'rU')
+        
+        #print "\nInput matrix path and name ", inputMatrixPath,"\n"
+        error= False
+
+        countRow=   0
+        lenRow1=    0
+        lenAllRows= 0
+        inMatrixRowLabels= []
+        inMatrixColLabels= []
+        
+        for rawRow in inMatrixFH:
+            countRow +=1
+            
+            rawRow= rawRow.replace('\n','')
+            eachRow=  rawRow.split('\t')
+            if countRow < 2: print 'Input Matrix start 1 to 10= ',eachRow[:10], '\n'
+            
+            if countRow == 1: 
+                lenRow1= len(eachRow)
+                inMatrixColLabels= eachRow
+                for j in range(1,lenRow1):
+                    tmp= re.search('[abcdefghijklmnopqrstuvwxyz]',eachRow[j].lower())
+                    try:
+                        if tmp.group(0) == '':  # if doesn't exist then error
+                            tmp= tmp
+                    except Exception as e:
+                        print("\n--+-+- ERROR Column Headers at position "+str(j+1)+" value appears to be non-alphanumeric --"+str(eachRow[j])+"--")
+                        sys.stderr.write("\n--+-+- ERROR Column Headers at position "+str(j+1)+" value appears to be non-alphanumeric --"+str(eachRow[j])+"--")
+                        error= True
+
+                if lenRow1 < 3:  # likely is covariate file not input matrix
+                    print"----WARNING Input  number of columns= " , str(lenRow1)," is too few likely input matrix is really a covariate file"
+                    SystemError ("----WARNING Input  number of columns= " + str(lenRow1)+" is too few likely input matrix is really a covariate file")
+                    #error= True
+                    #sys.err= 2
+            elif countRow == 2: 
+                lenAllRows= len(eachRow)
+                if (lenAllRows == lenRow1) or (lenAllRows == lenRow1+1):  #or (lenAllRows- lenRow1 == 0 or 1): 
+                    print"Validating Input matrix,  number of Labeled Columns = ", str(lenAllRows)
+                    inMatrixRowLabels.append(eachRow[0])
+
+#  allow other error to occur first
+#                     tmp= re.search('[abcdefghijklmnopqrstuvwxyz]',eachRow[0].lower())
+#                     try:
+#                         if tmp.group(0) == '':  # if doesn't exist then error
+#                             tmp= tmp
+#                     except Exception as e:
+#                         print("\n--+-+- WARNING Row Label at row 2 value appears to be non-alphanumeric --"+str(eachRow[j])+"--")
+#                         sys.stderr.write("\n--+-+- WARNING Row Label at row 2 value appears to be non-alphanumeric --"+str(eachRow[j])+"--")
+#                         #error= True
+                    if (lenAllRows == lenRow1) and (inMatrixColLabels[0]==''): inMatrixColLabels.pop(0)  #remove blank first cell
+
+                else: 
+                    print( "\n--ERROR  Input matrix number columns= "+str(lenRow1)+" in first row and the second row= "+str(lenAllRows)+" mismatch ")
+                    sys.stderr.write( "\n--ERROR  Input matrix number columns= "+str(lenRow1)+" in first row and the second row= "+str(lenAllRows)+" mismatch ")
+                    error= True
+                    sys.err= 6
+            elif (lenRow1 != len(eachRow) and lenRow1+1 != len(eachRow)):
+                    print ("\n--ERROR  Input Row "+ str(countRow)+" number of columns= "+str(len(eachRow))+" is a length mismatch with row 2 length "+str( lenAllRows))
+                    sys.stderr.write ("\n--ERROR  Input Row "+ str(countRow)+" number of columns= "+str(len(eachRow))+" is a length mismatch with row 2 length "+str( lenAllRows))
+                    error= True
+                    sys.err= 7
+            else:
+                inMatrixRowLabels.append(eachRow[0])
+                tmp= re.search('[abcdefghijklmnopqrstuvwxyz]',eachRow[0].lower())
+                try:
+                    if tmp.group(0) == '':  # if doesn't exist then error
+                        tmp= tmp
+                except Exception as e:
+                    print"-+-+- WARNING Row Label at row "+str(countRow)+" value appears to be non-alphanumeric --"+str(eachRow[j])
+                    sys.stderr.write("\n--+-+- WARNING Row Label at row "+str(countRow)+"  value appears to be non-alphanumeric "+str(eachRow[j]))
+                
+            
+            if len(inMatrixColLabels) > 0: 
+                if (inMatrixColLabels[-1] =='') or (inMatrixColLabels[-1] =='\n'): inMatrixColLabels.pop()
+     
+        inMatrixFH.close()
+
+            #print error, lenAllRows, len(eachRow), eachRow[0]
+     except:
+        #inMatrixFH.close()
+        sys.stderr.write(str(traceback.format_exc()))
+        error= True
+    
+     return error,inMatrixRowLabels,inMatrixColLabels
+
+ #+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-
+
+def ValidateHMCorvarFile(covarLabel, covariateFilePath, row_col_cat_contin, inMatrixRowLabels,inMatrixColLabels):           # This sub routine ensures that the slide design input by the user matches a slide design on record
+
+# verify 
+# 1 That covar file labels match the col or row labels 1 to 1
+# 2 That if a continuous covar file that the 2nd field is not all text hard to tell if '-' or 'e exponent'
+# 3 That the length of the covar file matches the row or col length of the input matrix 
+
+    error= True
+    try:
+    
+        covFH= open( covariateFilePath, 'rU')
+        countRow= 0
+
+        error= False
+        
+        for rawRow in covFH:
+            countRow +=1
+            rawRow= rawRow.replace('\n','')
+            eachRow=  rawRow.split('\t')
+            if countRow== 0: print "\nCovariance file info - label ",str(covarLabel)," row/col categorical or continous",row_col_cat_contin," first row ",str(eachrow)
+    
+            if len(eachRow) < 2 and countRow > 1:
+                print("----ERROR Input Row "+str(countRow)+" does not have a label and/or value ")
+                sys.stderr.write("----ERROR Input Row "+str(countRow)+" does not have a label/or and value")
+                error= True
+                sys.err= 8
+                #return error
+            elif len(eachRow) > 1:
+                tmp= re.search('[abcdefghijklmnopqrstuvwxyz]',eachRow[0].lower())
+                try:
+                    if tmp.group(0) == '':  # if doesn't exist then error
+                        tmp= tmp
+                except Exception as e:
+                    print"\n-+-+- WARNING Covariate Label at row "+str(countRow)+" value appears to be non-alphanumeric --", eachRow[0],"--"
+                    sys.stderr.write("\n--+-+- WARNING Row Headers at  row "+str(countRow)+" value appears to be non-alphanumeric --"+str(eachRow[0])+"--")
+                    
+                if not error:
+                    if row_col_cat_contin[-4:] == 'uous':  # verify continuous is number-ish
+                        tmp= re.search('[+-.0123456789eE]',eachRow[1])
+                        try:
+                            if tmp.group(0) == '':
+                                tmp= tmp
+                        except Exception as e:
+                            print("\n-+-+-WARNING Input Row "+str(countRow)+" covariance continuous value appears to be non-numeric --"+ str(eachRow[1])+"--")
+                            sys.stderr.write("\n-+-+-WARNING Input Row "+str(countRow)+" covariance continuous value appears to be non-numeric --"+ str(eachRow[1])+"--")
+                            #error= True
+    except:
+        sys.stderr.write(str(traceback.format_exc()))
+
+    covFH.close()
+
+    return error
+
+
+if __name__ == "__main__":
+    main()
+
+