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.
You're trying to pass file objects as filenames. Try using
infile = '110331_HS1A_1_rtTA.result'
outfile = '2.txt'
at the top of your code.
(Not only does the doubled usage of open()
cause that problem with trying to open the file again, it also means that infile
and outfile
are never closed during the course of execution, though they'll probably get closed once the program ends.)
Here is the best way I found for Python 2:
def inplace_change(file,old,new):
fin = open(file, "rt")
data = fin.read()
data = data.replace(old, new)
fin.close()
fin = open(file, "wt")
fin.write(data)
fin.close()
An example:
inplace_change('/var/www/html/info.txt','youtub','youtube')
For the less specific case (not just the code in the question - since this is one of the first results in Google for this generic error message. This error also occurs when running certain os command with None argument.
For example:
os.path.exists(arg)
os.stat(arg)
Will raise this exception when arg is None.
Source: Stackoverflow.com