Python mkdir issue, file exists error

Question

Im trying to create directories and a files within each folder, using data from an input file.

It works for the first one but then gives me the FileExistsError

I have been staring at this for hours now and just can't seem to get it, any help would be appreciated.

File data looks like this

>unique id
string of unknown length

and the code I've tried is this

import os


# find a character

CharLocArray = []

NewLineArray = []

with open('/home/tjbutler/software/I-TASSER5.0/seqdata/Egg_protein/seq.fasta', 'r') as myfile:

    data = myfile.read()
    GreaterThan = '>'
    NewLine = '\n'

    # code to read char into var
    # myfile.read().index('>')
    index = 0
    while index < len(data):
        index = data.find('>', index)
        CharLocArray.append(index)
        if index == -1:
            break

        index += 2

    index2 = 0
    while index2 < len(data):
        index2 = data.find('\n', index2)
        NewLineArray.append(index2)
        if index2 == -1:
            break

        index2 += 2

    i = 0
    print(len(CharLocArray))

    while i < len(CharLocArray):
        print(i)
        CurStr = data[CharLocArray[i]:]
        CurFolder = CurStr[CharLocArray[i]:NewLineArray[i]]
        print(CurFolder)
        CurData = CurStr[CharLocArray[i]:CharLocArray[i + 1]]
        print(CurData)
        newpath = r'/home/tjbutler/software/I-TASSER5.0/seqdata/Egg_protein/'
        DirLocation = newpath + CurFolder
        print(DirLocation)
        FileLocation = DirLocation + '/seq.fasta'
        print(FileLocation)
        i = i + 1
        print(i)
        if not os.makedirs(DirLocation):
            os.makedirs(DirLocation)
            file = open(FileLocation, 'w+')
            file.write(CurData)
            file.close()

zwer · Accepted Answer · 2017-07-03 23:25:51Z

3

os.makedirs() should not be used that way - use its exist_ok argument instead:

    os.makedirs(DirLocation, exist_ok=True)  # instead of the condition!
    with open(FileLocation, 'w+') as f:
        f.write(CurData)

also, don't manually create your own paths (i.e. FileLocation = DirLocation + '/seq.fasta'), use os.path facilities instead, e.g.: FileLocation = os.path.join(DirLocation, seq.fasta).

answered Jul 3, 2017 at 23:25

zwer

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