Function does not work properly in for loop - Python

Question

I have a text file in the following format:

AAAAATTTTTT
AAATTTTTTGGG
TTTDDDCCVVVVV

I am trying to calculate the number of occurrences of a character in sequence at start and end of the line.

I have written the following function:

def getStartEnd(sequence):
    start = sequence[0]
    end = sequence[-1]
    startCount = 0
    endCount = 0

    for char in sequence:
        if char == start:
            startCount += 1
            if ( char != start):
                break

    for char in reversed(sequence):
        if char == end:
            endCount += 1
            if ( char != end):
                break

    return startCount, endCount

This function works independently on strings. For e.g.:

seq = "TTTDDDCCVVVVV"
a,b = getStartEnd(seq)
print a,b

But when I insert in a for loop, it gives the correct value only on the last line of the file.

file = open("Test.txt", 'r')

for line in file:
    a,b = getStartEnd(str(line))
    print a, b

falsetru · Accepted Answer · 2013-10-03 05:47:31Z

3

Because lines except the last line, contains newlines.

Try following (strip trailing spaces):

with open("Test.txt", 'r') as f:
    for line in f:
        a, b = getStartEnd(line.rstrip())
        print a, b

BTW, ( char != end ) in the following code is always False. (same for the ( char != start))

for char in reversed(sequence):
    if char == end:
        endCount += 1
        if ( char != end): # always False because char == end
            break

Do you mean this?

for char in reversed(sequence):
    if char == end:
        endCount += 1
    else:
        break

How about using itertools.takewhile:

import itertools

def getStartEnd(sequence):
    start = sequence[0]
    end = sequence[-1]
    start_count = sum(1 for _ in itertools.takewhile(lambda ch: ch == start, sequence))
    end_count = sum(1 for _ in itertools.takewhile(lambda ch: ch == end, reversed(sequence)))
    return start_count, end_count

edited Oct 3, 2013 at 5:47

answered Oct 3, 2013 at 5:37

falsetru

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2 Comments

gthm Over a year ago

Thank you very much. How about my code ? Is it an elegant way ?

gthm Over a year ago

I want to count the first char in sequence. For eg: AAAATTAGGAGGG, the starting letter A is occuring 4 times, and end letter G occuring 3 time in continuous order.

Shashank · Accepted Answer · 2013-10-03 05:43:09Z

1

Three things. First, in your function, you probably meant to break using the following structure.

for char in sequence:
    if char == start:
        startCount += 1
    else:
        break

for char in reversed(sequence):
    if char == end:
        endCount += 1
    else:
        break

Second, when you are looping through the lines in your file, you don't need to convert the lines to strings with the str function. They already are strings!

Third, the lines include newline characters which are like this: '\n' They are used to tell the computer when to end a line and start a new one. To get rid of them, you can use the rstrip method of string as follows:

file = open("Test.txt", 'r')

for line in file:
    a,b = getStartEnd(line.rstrip())
    print a, b
file.close()

answered Oct 3, 2013 at 5:43

Shashank

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1 Comment

falsetru Over a year ago

Fourth, use with statement.

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