problems removing newline character in python

Question

I've also tried using newString.strip('\n') in addition to the ones already in the code, but it doesn't do anything. I am inputing a .fasta file which shouldn't be a problem. Thanks in advance.

def createLists(fil3):
    f = open(fil3, "r")
    text = f.read()

    listOfSpecies = []
    listOfSequences = []

    i = 0
    check = 0

    while (check != -1):
        startIndex = text.find(">",i)
        endIndex = text.find("\n",i)
        listOfSpecies.append(text[startIndex+1:endIndex])

        if(text.find(">",endIndex) != -1):
            i = text.find(">",endIndex)
            newString = text[endIndex+1: i]
            newString.strip()
            newString.splitlines()
            listOfSequences.append(newString)

        else:
            newString = text[endIndex+1:]
            newString.strip()
            newString.strip('\n')
            listOfSequences.append(newString)
            return (listOfSpecies,listOfSequences)


def cluster(fil3):
    print createLists(fil3)


cluster("ProteinSequencesAligned.fasta")

I have and there is no difference before and after the strip which seems odd to me — Alberto Does, May 06 '12 at 06:39
Try print repr(newString) before and after strip, if it doesn't show \n before strip then the string never had a newline — Roman A. Taycher, May 06 '12 at 06:44
>Baboon -VHLTPEEKNAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFDSFGDLSSPAAVMGNPKVKAHGKKVLGAF SDGLNHLDNLKGTFAQLSELHCDKLHVDPENFKLLGNVLVCVLAHHFGKEFTPQVQAAYQKVVAGVANALAH KYH >Galago -VHLTPDEKNAVCALWGKVNVEEVGGEALGRLLVVYPWTQRFFDSFGDLSSPSAVMGNPKVKAHGKKVLSAF SDGLQHLDNLCGTFAKLSELHCDKLHVNPENFRLLGNVLVCVLAHHFGKDFTPEVQAAYEKVVAGVATALAH KYH >Colobus MVHLTPDEKAAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSSPDAVMGNPKVKAHGKKVLGAF SDGLAHLDNLKGTFAQLSELHCDKLHVDPENFKLLGNVLVCVLAHHFGKEFTPQVQAAYQKVVAGVANALAH KYH — Alberto Does, May 06 '12 at 06:46
If the newline is not at the end strip wont do anything(strip strips from right and left ends. splitline gets rid of newlines — Roman A. Taycher, May 06 '12 at 06:49
When you have read the file, you should close it with `f.close()`. — akaRem, May 06 '12 at 11:07

score 4 · Accepted Answer · answered May 06 '12 at 07:00

4

Strings are immutable:

In [1]: s = 'lala\n'

In [2]: s.strip()
Out[2]: 'lala'

In [3]: s
Out[3]: 'lala\n'

In [4]: s = s.strip()

In [5]: s
Out[5]: 'lala'

So just do:

new_string = text[end_index+1:].strip()

And please follow PEP 8. Also, you could rewrite your loop just using a for loop over the lines. Python files support direct iteration:

In [6]: with open('download.py') as fobj:
   ...:     for line in fobj:
   ...:         print line

And if you don't use the with statement, make sure you close the file with the close() method at the end of your function.

answered May 06 '12 at 07:00

rubik

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Edited to give a couple of suggestions. – rubik May 06 '12 at 07:04
Thank you, I just replaced the strip with splitlines. Also is the PEP 8 comment in reference to the naming of newString rather than new_string? – Alberto Does May 06 '12 at 07:16
@AlbertoDoes: It's a general advice: most for variables naming, but also for spaces (for example around operators), or conditionals (`if cond or cond2` is better than `if(cond) or (cond2)`). – rubik May 06 '12 at 07:20
Great, thanks for the advice. I didn't realize the splitline method made new additions to the list. I found a way around the problem by using new_string = text[endIndex+1:].replace('\n', '') – Alberto Does May 06 '12 at 07:26

score 0 · Answer 2 · answered May 06 '12 at 16:56

0

Well In the end I found the best solution to be new_string = text[endIndex+1:].replace('\n', '')

answered May 06 '12 at 16:56

Alberto Does

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problems removing newline character in python

2 Answers2