Also, you should use a for loop OR a while loop, but not both. A for loop with a break statement to stop the loop early is probably best.

lines = open(filename).read().splitlines()

You can read the whole file and split lines using str.splitlines:

temp = file.read().splitlines()

Or you can strip the newline by hand:

temp = [line[:-1] for line in file]

Note: this last solution only works if the file ends with a newline, otherwise the last line will lose a character.

This assumption is true in most cases (especially for files created by text editors, which often do add an ending newline anyway).

If you want to avoid this you can add a newline at the end of file:

with open(the_file, 'r+') as f:
    f.seek(-1, 2)  # go at the end of the file
    if f.read(1) != '\n':
        # add missing newline if not already present
        f.write('\n')
        f.flush()
        f.seek(0)
    lines = [line[:-1] for line in f]

Or a simpler alternative is to strip the newline instead:

[line.rstrip('\n') for line in file]

Or even, although pretty unreadable:

[line[:-(line[-1] == '\n') or len(line)+1] for line in file]

Which exploits the fact that the return value of or isn't a boolean, but the object that was evaluated true or false.

The readlines method is actually equivalent to:

def readlines(self):
    lines = []
    for line in iter(self.readline, ''):
        lines.append(line)
    return lines

# or equivalently

def readlines(self):
    lines = []
    while True:
        line = self.readline()
        if not line:
            break
        lines.append(line)
    return lines

Since readline() keeps the newline also readlines() keeps it.

Note: for symmetry to readlines() the writelines() method does not add ending newlines, so f2.writelines(f.readlines()) produces an exact copy of f in f2.

Read line by line. Use #main as a flag to start processing. Use #extra as a flag to stop processing.

start = '#main'
end = '#extra'
numbers = []
file_handler = open('read_up_to_a_point.txt')
started = False
for line in file_handler:
    if end in line:
        started = False       
    if started:
        numbers.append(line.strip())
    if start in line:
        started = True
file_handler.close()
print numbers

sample output

python read_up_to_a_point.py ['60258960', '33031674', '72302403']

If you are using Python 3.8, you could utilise the walrus operator here

ls = []

while (inp := input("> ")):
    ls.append(inp)

print(ls)

files are iterators (unlike lists) so you can just make a second for loop:

with open(inputfile, 'r') as infile:
    for line in infile:
        if line.startswith(">"):
            print line, # comma on the end prevents the double spacing from printing a file line
            for line in infile:
                print line,
                if line.startswith(">"):
                    break # stop this inner for loop; outer loop picks up on the next line

Edit: I get the feeling I don't understand your problem. Can you show some example data and what you want out?

Probably the slickest way that I know (with no error handling, unfortunately, which is why you don't see it too often in production):

>>> lines = list(iter(input, ''))
abc
def
.
g

>>> lines
['abc', 'def', '.', 'g']

This uses the two-parameter call signature for iter, which calls the first argument (input) until it returns the second argument (here '', the empty string).

Your way's not too bad, although it's more often seen under the variation

a = []
while True:
    b = input("->")
    if not b:
        break
    a.append(b)

Actually, use of break and continue is one of the rare cases where many people do a one-line if, e.g.

a = []
while True:
    b = input("->")
    if not b: break
    a.append(b)

although this is Officially Frowned Upon(tm).

This is pretty straight forward, you can terminate a loop early with a break statement.

filename = 'somefile.txt'

with open(filename, 'r') as input:
   for line in input:
       if 'indicator' in line:
            break

Using with creates a compound statement that ensures that upon entering and leaving the scope of the with statement __enter__() and __exit__() will be called respectively. For the purpose of file reading this will prevent any dangling filehandles.

The break statement tells the loop to terminate immediately.