Can't copy compressed files

Question

I need to copy various files for several times with a specific name and I wanted to make the process automate. This is my python code:

number_of_copies = int(raw_input("enter number of copies "))

copy_number = 1

infile = raw_input("file to be copied ")
new_file = raw_input("What's the name of the new file?")
extension = ".fastq"
indata = open(infile)

file_to_copy = str(indata.read())

while copy_number < number_of_copies:

    copy = open(new_file + "-" + str(copy_number) + extension, 'w')
    copy.write(file_to_copy)
    copy_number = copy_number + 1    

indata.close()
copy.close()

In this case I know the extension of my file so I have hard coded it and I just change that variable in the script accordingly. The script works fine with my .fastq files (basically text files) but as soon as I try it on a fastq.gz file (compressed) the copy has size 1kb (from original >300 Mb size). I believe the problem is with the fact that the .gz is a compressed file but I don't know how to solve this. Any help is greatly appreciated.

p.s. of course, when I try it with the .gz files I change the "extension" variable as well.

Thank you in advance!

Check this link https://docs.python.org/2/library/shutil.html, I think better to use function shutil.copyfile — Oleksandr Dashkov, Oct 31 '16 at 09:35
Yes, taken from the documentation 'On Windows, file owners, ACLs and alternate data streams are not copied.' — Oleksandr Dashkov, Oct 31 '16 at 10:03
Also see http://stackoverflow.com/questions/16627465/copying-files-with-python — PM 2Ring, Oct 31 '16 at 10:05
Thank you! I had a look at that! Pretty interesting and useful indeed! — Faber, Oct 31 '16 at 10:06

score 2 · Accepted Answer · edited May 23 '17 at 11:48

2

As noted in the comments, using shutil is more efficient.

You're getting errors because your OS does newline translation on text files. So to use the above code correctly on all files you need to open them in binary mode, eg

open(infile, 'rb')

and

open(new_file + "-" + str(copy_number) + extension, 'wb')

Here are the Python 2 docs for open. And this answer has a handy table of the standard file modes.

edited May 23 '17 at 11:48

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answered Oct 31 '16 at 09:53

PM 2Ring

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@Faber No worries. I've added a couple of Python 2 links to my answer. BTW, you should seriously consider moving to Python 3 because Python 2 won't be supported after 2020. – PM 2Ring Oct 31 '16 at 10:13

score -1 · Answer 2 · answered Oct 31 '16 at 09:48

with open('recipes.tar.gz', 'r') as raw_file:
    with open('new.gz', 'w') as new_file:
        new_file.write(raw_file.read())

I think your question is can't open the ".gz" extension file, so I try it, does not happened any problem. Of course if your file is very lage, it will be another problem.

Can't copy compressed files

2 Answers2