TypeError: coercing to Unicode: need string or buffer

Question

This code returns the following error message:

• with open (infile, mode='r', buffering=-1) as in_f, open (outfile, mode='w', buffering=-1) as out_f: TypeError: coercing to Unicode: need string or buffer, file found

  # Opens each file to read/modify
  infile=open('110331_HS1A_1_rtTA.result','r')
  outfile=open('2.txt','w')
  
  import re
  
  with open (infile, mode='r', buffering=-1) as in_f, open (outfile, mode='w', buffering=-1) as out_f:
      f = (i for i in in_f if i.rstrip())
      for line in f:
          _, k = line.split('\t',1)
          x = re.findall(r'^1..100\t([+-])chr(\d+):(\d+)\.\.(\d+).+$',k)
          if not x:
              continue
          out_f.write(' '.join(x[0]) + '\n')
  

Please someone help me.

Answer 1

You're trying to open each file twice! First you do:

infile=open('110331_HS1A_1_rtTA.result','r')

and then you pass infile (which is a file object) to the open function again:

with open (infile, mode='r', buffering=-1)

open is of course expecting its first argument to be a file name, not an opened file!

Open the file once only and you should be fine.