new_contents: # -*- coding: utf-8 -*-
  """
  Created on Mon Feb 20 17:09:40 2017
  
  Make config templates for MIRA assemblies
  for entire plate and well
  This is slowly becoming library of repeatedly used functions
  @author: tcampbell
  """
  
  
  import os
  import sys
  import re
  from FindFastaFiles import findmorphs as dblook
  
  
  path = '/home/tcampbell/ENVTC/'
  
  sys.path.append(path)
  
  def writefile(fastqfile, directory, library, plate, well, bcname):
  #    global plate
      cname = directory +  library + '/' + plate + '/'
  #    coname = directory + out + library + '/' + plate + '/'
      templatefile = cname  +  plate +'_'+ well + "_" +  bcname + '_miratemp_3.txt'
      if os.path.exists(cname) == True and os.path.isfile(templatefile) == False:#make something that warns that file exists, ask to overwrite
  #        print cname +  plate +'_'+ well + '_'+ bcname + '_miratemp.txt'
          with open(templatefile, 'w') as export:
  #        num =range(len(files))
  #        export.write('[')
  #        for no in num:
                  record = 'project = ' + plate + '_' + well+' \n\
  job = genome, denovo, accurate \n\
  \n\
  readgroup = '+ plate + '_' + well + ' \n\
  data='+ directory + fastqfile + ' \n\
  technology = iontor \n\
  \n\
  parameters = COMMON_SETTINGS -GENERAL:number_of_threads = 1 \ \n\
                               -CO:mr=yes \ \n\
                               -ASSEMBLY:num_of_passes=3:spoiler_detection=on:use_emergency_search_stop=off\ \n\
                               -NW:check_duplicate_readnames=no \ \n\
               IONTOR_SETTINGS -ASSEMBLY:minimum_read_length=50 \ \n\
                               -ALIGN:min_relative_score=60 \ \n\
                               -CO:mgqrt=35 \ '
                  export.write(str(record))
  #            if len(files)-no >= 2:
  #                export.write(',')
  #        export.write('\n]')    
                  export.close  
  #         -DIR:tmp_redirected_to=/home/tcampbell/ENVTC/MIRA/temp \ \n\ #removed from common settings
      else:
          print "Mira Template Filepath Out " + cname + " does not exist."
          
  def fastqfilefinder(directory):
  #    subprocess.check_call(["ls"])
  #    subprocess.check_output("exit 1", shell=True)
      os.system("'ls' "+ directory + " > " + directory + "fastqfilelist.txt")
      
      
  def readfiles(fastqfilelist):
      with open(fastqfilelist, 'rb') as tsvin:
          tsvin = tsvin.csvread(tsvin, delimiter='\t')
  #   
          for row in tsvin:
              well= str(row)
              plate = test
              bcname = 'Geller'
              if re.search(r'seqs_[0-9]{2}[A-H].fastq', well):
                  p= re.search(r'seqs_([0-9]{2}[A-H]).fastq', well)                
                  writefile(p.group(0), directory, plate, p.group(1), bcname)
                  print "Match"
              else:
                  print "NO MATCH"
  
  def mysqlconnect(connectionpath): #uses the information in the connection file to open mysql connection
      connect = open(connectionpath, 'r')
  #    print cnx.read()
      cnx = connect.read()
      cnx.strip('\n')
      return cnx
  
  
  
  def main():
      
      ###=============THIS WORKS FOR READING FASTQ FILES TO MAKE MIRA TEMPLATE================################   
      
      directory = "/path/to/fastq/files/"
      fastqfilefinder(directory) 
      readfiles(directory + "fastqfilelist.txt") 
      ###=============THIS WORKS FOR READING FASTQ FILES TO MAKE MIRA TEMPLATE (END)================################  
  
      connect = mysqlconnect('/path/to/connectionfile.tsv')
  
      cnx =  connect #makes variable declaration a string
      exec(cnx) #executes declaration of variable using string from previous step
  
  
      cursor = cnx.cursor()
  
      
  
      cursor.close()
      cnx.close()
      
      
  if __name__ == "__main__":
      morphiles = main()    
      
  
  
subject: Create MIRA_templateFilewriter.py