--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Split_ExcelTabs_IntoFiles.py	Tue Nov 27 14:20:40 2018 -0500
@@ -0,0 +1,290 @@
+import sys
+import os
+#import MySQLdb
+#import config
+import subprocess
+import re
+import shutil
+import traceback
+#import xlsxwriter
+import xlrd
+
+#http://www.blog.pythonlibrary.org/2014/04/30/reading-excel-spreadsheets-with-python-and-xlrd/
+
+def File_From_Tab(infileName, outfileName, tabName,tabNumber):
+    """
+    Open and read an Excel file
+    """
+    book = xlrd.open_workbook(infileName)
+    # print number of sheets
+    #print book.nsheets
+ 
+    # print sheet names
+    tabList= book.sheet_names()
+    #print tabList
+    #print book.sheet_names()
+    if tabName == "" and (tabNumber <1 or tabNumber > len(tabList)):
+        sys.stderr.write("\n>>>ERROR illegal tab number "+str(tabNumber)+" input when no tab name was specified\n")
+        sys.stderr.write("\n>>>Allowed tab numbers, or tab names, for this file with "+str(len(tabList))+" total tabs are:")
+        
+        for i in range(len(tabList)):
+            sys.stderr.write("\n>>>   tab number "+str(i+1)+" is named "+str(tabList[i]))
+        sys.exit(-1)
+
+    if tabName != "":   # use name instead of tab number
+        found = False
+        i = 0
+        while (i < len(tabList)) and not found:
+            i += 1
+            if tabName == str(tabList[i-1]):
+                tabNumber = i
+                found = True
+        if not found:
+            sys.stderr("\n>>> ERROR -- Input Tab name "+tabName+" was not found\n")
+            sys.exit(-1)
+    # get the first worksheet
+    #first_sheet = book.sheet_by_index(0)
+    worksheet = book.sheet_by_index(tabNumber-1)
+ 
+    outFile = open(outfileName+str(tabList[tabNumber-1]+".tsv"), 'w')
+   
+    #https://stackoverflow.com/questions/14944623/python-xrld-read-rows-and-columns
+    #workbook = xlrd.open_workbook('my_workbook.xls')
+    #worksheet = workbook.sheet_by_name('Sheet1')
+    num_rows = worksheet.nrows - 1
+    num_cells = worksheet.ncols - 1
+    curr_row = -1
+    while curr_row < num_rows:
+      curr_row += 1
+      row = worksheet.row(curr_row)
+      
+      if curr_row == 0:
+          endOfLine= False
+          allRowNumCols= len(row)
+          i= len(row)-1
+          # find length of matrix and covariates using first row 
+          # Cell Types: 0=Empty, 1=Text, 2=Number, 3=Date, 4=Boolean, 5=Error, 6=Blank
+          while i <= len(row)-1 and not endOfLine:
+               cell_type = worksheet.cell_type(curr_row, i)
+               #temp = str(worksheet.cell_value(curr_row, i))
+               #print( " pos and cell type row one ",cell_type, i)
+               
+               if cell_type == 0 or cell_type == 6:
+                  allRowNumCols -= 1
+                  i -= 1
+               else:
+                  endOfLine=  True
+         
+      if allRowNumCols < 5:
+          sys.stderr.write("\nERROR First row number of columns= "+str(allRowNumCols)+" is too short, so all rows will be ignored\n")
+          sys.exit(-1)
+      elif curr_row == 0: 
+          sys.stdout.write("\nALL Rows must all have the same number of columns as the First row's number columns = "+ str(allRowNumCols) +"\n")
+          
+      temp= ''
+      rowLen= 0
+      endOfLine= False
+          
+      while rowLen < allRowNumCols and not endOfLine:
+          temp += str(worksheet.cell_value(curr_row, rowLen))+"\t"
+          #temp += str(row[rowLen])+"\t"
+          rowLen += 1
+              
+      temp = temp[:-1]+"\n"
+      #print 'Row:', curr_row, len(row), rowLen
+      outFile.write(temp)  #TODO check if rows are all same length
+    
+    sys.stdout.write("File created with "+str(curr_row)+" rows and "+str(allRowNumCols)+" columns\n")
+#       curr_cell = -1
+#       while curr_cell < num_cells:
+#         curr_cell += 1
+#         # Cell Types: 0=Empty, 1=Text, 2=Number, 3=Date, 4=Boolean, 5=Error, 6=Blank
+#         cell_type = worksheet.cell_type(curr_row, curr_cell)
+#         cell_value = worksheet.cell_value(curr_row, curr_cell)
+#         print ' ', cell_type, ':', cell_value 
+    #     # read a row
+#     print first_sheet.row_values(0)
+#  
+#     # read a cell
+#     cell = first_sheet.cell(0,0)
+#     print cell
+#     print cell.value
+#  
+#     # read a row slice
+#     print first_sheet.row_slice(rowx=0,
+#                                 start_colx=0,
+#                                 end_colx=2)
+ 
+    return tabList
+
+
+#======================
+# from RPPA callInSilicoReportWriter.py
+# def write_xlsx_for_report(directory_for_reports, report_name, report_id, dict_cf2_values):
+#     
+#     
+#     error_write_xlsx = ""
+#     error_occurred = 0
+#     
+#     try:
+#         path_to_dir_when_writing = os.path.join(directory_for_reports, report_name)
+#         header_path = os.path.join(directory_for_reports, report_name, "header.csv")    
+#         raw_log_2_path = os.path.join(directory_for_reports, report_name, "RawLog2.csv")
+#         norm_linear_path = os.path.join(directory_for_reports, report_name, "NormLinear.csv")
+#         norm_log_2_path = os.path.join(directory_for_reports, report_name, "NormLog2.csv")
+#         norm_log_2_median_centered_path = os.path.join(directory_for_reports, report_name, "NormLog2_MedianCentered.csv")
+#         
+# #         put the cf2 values in the NormLinear file
+#         error_put_cf2_in_normLinear = write_new_normLinear_csv_file_with_cf2_values(path_to_dir_when_writing, norm_linear_path, dict_cf2_values)
+#         
+#         
+#         excel_workBook = xlsxwriter.Workbook(os.path.join(directory_for_reports, report_name,report_name + ".xlsx"), {'strings_to_numbers': True})
+#     
+#         rawLog2_worksheet = excel_workBook.add_worksheet("RawLog2")
+#         error_rawLog2 = construct_worksheet_for_xlsx(rawLog2_worksheet, header_path, "RawLog2", raw_log_2_path)
+#     
+#         norm_linear_worksheet = excel_workBook.add_worksheet("NormLinear")
+#         error_norm_linear = construct_worksheet_for_xlsx(norm_linear_worksheet, header_path, "NormLinear", norm_linear_path)
+#     
+#         norm_log_2_worksheet = excel_workBook.add_worksheet("NormLog2")
+#         error_norm_log_2 = construct_worksheet_for_xlsx(norm_log_2_worksheet, header_path, "NormLog2", norm_log_2_path)
+#     
+#         norm_log_2_median_centered_worksheet = excel_workBook.add_worksheet("NormLog2_MedianCentered")
+#         error_norm_log_2_median_centered = construct_worksheet_for_xlsx(norm_log_2_median_centered_worksheet, header_path, "Median-Centered", norm_log_2_median_centered_path)
+#     
+#         errors_array = [error_put_cf2_in_normLinear, error_rawLog2, error_norm_linear, error_norm_log_2, error_norm_log_2_median_centered]
+#         for error in errors_array:
+#             if error != "":
+#                 error_write_xlsx = error_write_xlsx + error
+#                 error_occurred = 1
+#         if error_occurred == 1:
+#             error_write_xlsx + "\nThe excel workbook for the report "+report_name+" was not written successfully.\n\n"
+#         
+#         excel_workBook.close()
+#     except Exception, e:
+#         error_occurred = 1
+#         error_write_xlsx += str(repr(e)) + "\n\n"
+#         error_write_xlsx + "\nThe excel workbook for the report "+report_name+" was not written successfully.\n\n"
+#         try:
+#             excel_workBook.close()
+#         except Exception, f:
+#             sys.stderr.write("An unforeseen problem has occurred in write_xlsx_for_report()\n")
+#             sys.stderr.write(str(repr(f)) + "\n\n")
+#         
+#     
+#     return error_occurred, error_write_xlsx
+# 
+# 
+# def write_new_normLinear_csv_file_with_cf2_values(path_to_dir, norm_linear_path, dict_cf2_values):
+#     errors = ""
+#     try:
+#         titles = {}
+#         new_lines_normLinear_with_cf2 = []
+#     #     read old norm linear file
+#         rf_normLinear = open(norm_linear_path, 'rU')
+#         line_num = 0
+#         for line in rf_normLinear:
+#             line = strip_new_line_from_right_side(line)
+#             toks = line.split(",")
+#             line_num += 1
+#             if line_num == 1:
+#                 line += "1,CF2"
+#                 new_lines_normLinear_with_cf2.append(line)
+#                 titles = toks
+#                 continue
+#             pos_rf = int(toks[titles.index('Order')])
+#             line += "," + str(dict_cf2_values[pos_rf])
+#             new_lines_normLinear_with_cf2.append(line)
+#         rf_normLinear.close()
+#     #     rename the old normLinear file
+#         os.rename(norm_linear_path, os.path.join(path_to_dir, 'before_cf2_NormLinear.csv'))
+#         
+#     #     write new normLinear with cf2
+#         wf_new_normLinear = open(norm_linear_path, 'w')
+#         for line_writing in new_lines_normLinear_with_cf2:
+#             wf_new_normLinear.write(line_writing + "\n")
+#         wf_new_normLinear.close()
+#     except Exception, err_write_normLinear_with_cf2_values:
+#         errors = str(repr(err_write_normLinear_with_cf2_values))
+# 
+#     return errors
+# 
+# 
+# # This function constructs the worksheet for each tab in the excel file for a report
+# # It puts these things in this order:
+# #     1. Title of the tab
+# #     2. Header for the tab
+# #     3. Content of the tab
+# def construct_worksheet_for_xlsx(worksheet, header_path, title_top_of_tab, tab_input_path):
+# 
+#     reload(sys)  
+#     sys.setdefaultencoding('utf8')
+#     errors = ""
+#     
+#     try:
+# #         Write the title at the top of the tab
+#         worksheet.write(0,0,title_top_of_tab)
+# 
+# #         Variable to keep track of the rows
+#         row_num = 1
+#         
+# #         Write the header stuff
+#         header_file = open(header_path, 'rU')
+#         for head_line in header_file:
+#             head_line = strip_new_line_from_right_side(head_line)
+#             head_toks = head_line.split(",")
+#             col_num = 0
+#             for tok in head_toks:
+#                 worksheet.write(row_num, col_num, tok)
+#                 col_num += 1
+#             row_num += 1
+#         
+# #         Write the content stuff
+#         tab_input_file = open(tab_input_path, 'rU')
+#         for tab_line in tab_input_file:
+#             tab_line = strip_new_line_from_right_side(tab_line)
+#             tab_toks = tab_line.split(",")
+#             col_num = 0
+#             for tok in tab_toks:
+#                 tok = tok.decode('iso-8859-1').encode('utf-8')
+#                 worksheet.write(row_num, col_num, tok)
+#                 col_num += 1
+#             row_num += 1        
+#         
+#         header_file.close()
+#         tab_input_file.close()
+#     except Exception, e:
+#         errors = errors + "\n\nAn error occurred while constructing the "+title_top_of_tab+" tab for the excel file.\n"
+#         errors = errors + "The error was :\n\t" + str(e) + "\n\n"
+#         try:
+#             header_file.close()
+#             tab_input_file.close()
+#         except NameError:
+#             x = 5
+#     
+    return errors
+
+#----------------------------------------------------------------------
+if __name__ == "__main__":
+    
+    #try:
+    if len(sys.argv) > 4:
+        infileName            = '"'+sys.argv[1]+'"'
+        tabName               = '"'+sys.argv[2]+'"' 
+        tabNumber = 0           
+        if tabName == '':  tabNumber = int(sys.argv[3])           
+        outfileName           = '"'+sys.argv[4]+'"'  #TODO Later multiple outputs one per tab
+          
+        sys.stdout.write( "\nInput parameters ",str(sys.argv[1:4]),"\n" )
+        
+    #infileName = "/Users/bobbrown/Desktop/01_Gordon_Mills__Zhiyong_Ding.xlsx"
+    #outfileName= "/Users/bobbrown/Desktop/01_Gordon_Mills__Zhiyong_Ding-Tab-Out-"
+    #tabName ="NormLog2"
+    #tabName =""
+    #tabNumber= 10
+        
+    status=  File_From_Tab(infileName, outfileName, tabName, tabNumber )
+    #except
+        #sys.exit(-1)
+    
+    sys.exit(0)
\ No newline at end of file