I think you have some slicing issues for example lets say your input is 12 0.1 0.1 0.25 line[1:] is going to be 2 0.1 0.1 0.25 because your input is a string. You can use something like:

line = '12 0.1 0.1 0.25'.split(' ') #convert your string to a list

temp = int(line[0]) #get first element and convert to integer to make comparisons easier

if temp < 3:
    print(' '.join(line))
elif temp == 5: 
    line[0] = '4'
    print(' '.join(line))
elif temp == 7:
    line[0] = '5'
    print(' '.join(line))
elif temp > 8:
    line[0] =str(temp - 3)
    print(' '.join(line))

#Output: 

9 0.1 0.1 0.25

Note: It's better to use elif instead of if in your case because if one of your conditions are true it is not going to check rest of the conditions. More info here

This is one approach.

Ex:

for file_name in list_of_files:
    data = []
    with open(file_name) as infile:
        for line in infile:
            if line.startswith("2 "):              #Check line
                line = " ".join(['7'] + line.split()[1:])   #Update line
            data.append(line)

    with open(file_name, "w") as outfile:     #Write back to file
        for line in data:
            outfile.write(line+"\n")

You can only read the whole file, call .replace() for the first line and write it to the new file.

with open('in.txt') as fin:
    lines = fin.readlines()
lines[0] = lines[0].replace('old_value', 'new_value')

with open('out.txt', 'w') as fout:
    for line in lines:
        fout.write(line)

If your file isn't really big, you can use just .join():

with open('out.txt', 'w') as fout:
    fout.write(''.join(lines))

And if it is really big, you would probably better read and write lines simultaneously.

Rather than trimming a fixed amount of characters from the beginning of the line, you can trim up to the first comma:

def line_restructure():                                                                                                 
    with open("Student_Directory.txt", "r") as f:                                                                       
        x = 1                                     #Sets starting line to 1                                                           
    output = []
    for line in f:
        index_of_comma = line.index(",")
        new = str(x) + line[index_of_comma:]  #Replaces portion of line up to first comma with X
        output.append(new)                    #Adds new string with replacement to output list
        x += 1                                #X becomes next line number

with open("Student_Directory.txt", "w") as f:
    f.writelines(output)                      #Rewrites file with same information
                                              #but first character == line number

You can use the readlines and writelines to do this. For example, I created a file called "test.txt" that contains two lines (in Out[3]). After opening the file, I can use f.readlines() to get all lines in a list of string format. Then, the only thing I need to do is to replace the first element of the string to whatever I want, and then write back.

with open("test.txt") as f:
    lines = f.readlines()

lines # ['This is the first line.\n', 'This is the second line.\n']

lines[0] = "This is the line that's replaced.\n"

lines # ["This is the line that's replaced.\n", 'This is the second line.\n']

with open("test.txt", "w") as f:
    f.writelines(lines)

Try this:)

for rf in glob.glob('./labels/train/*'):
    read=open(rf,'r')
    t=read.readlines()

    read.close()
    for_write = [str(int(ind[0])-1)+ind[1:] for ind in t]   
    write = open(rf,'w')
    write.writelines(for_write)
    write.close()

or using with:)

for rf in glob.glob('./labels/train/*'):
    with open('test.txt','r')as read:
        t=read.readlines()
        for_write = [str(int(ind[0])-1)+ind[1:] for ind in t]
    with open('test.txt','w') as write:
        write.writelines(for_write)

You should use just one loop. Read each file, make the changes you want, then rewrite the file.

You can use a regular expression to replace 1 at the start of each line.

import re
import glob
import os

for filename in glob.glob(os.path.join(source, '*.txt')):
    with open(filename, "r") as f:
        contents = f.read()
    contents = re.sub(r'^1', '0', contents, flags = re.MULTILINE)
    with open(filename, "w") as f:
        f.write(contents)

You shouldn't use os.path.join(getcwd(), filename). The files are in the source directory, not the current directory, and glob.glob() returns those pathnames.

When you are calling replace() it replaces every instance of that character in the string. Instead, just isolate the first character using [0] so that it will only replace there. e.g:

this_file.write(line[0].replace(s,'2'))

EDIT: I see that someone commented the same thing as i was typing mine

you are not using method calls properly. ie, you are defining stringMix as a function, but using variables that are out of the scope of the function. I think what you are trying to do is:

def stringMix(a,b):
  print (a.replace([0:2]b[0:2]))
  print (b.replace([0:2],a[0:2]))

userStringA = input("Please enter a string consisting of over two characters ")
userStringB = input("Please enter a second string consisting of over two characters ")

print (userStringA)
print (userStringB)

stringMix(userStringA,userStringB)

However, as previous answers and comments suggest, str.replace is not really the way to do this. you should instead do:

def stringMix(a,b):
  print (a[0:2]+b[2:])
  print (b[0:2]+a[2:])

to take advantage of string slicing and concatenating