On Sun, May 18, 2014 at 9:44 PM, Ian Kelly wrote:
> You can just use bz2.open:
>
> >>> with bz2.open('test.txt.bz2', 'rt', encoding='ascii') as f:
> ... print(f.read())
>
Thanks I like that better then my solution.
Vincent Davis
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On Sun, May 18, 2014 at 8:38 PM, Vincent Davis wrote:
> Well after posting, I think I figured it out.
> The key is to use StringIO to get a file handle on the string. The fact that
> it is binary just complicates it a little.
>
> with open('Tests/Affy/affy_v3_ex.CEL.bz2', 'rb') as handle:
> ce
Well after posting, I think I figured it out.
The key is to use StringIO to get a file handle on the string. The fact
that it is binary just complicates it a little.
with open('Tests/Affy/affy_v3_ex.CEL.bz2', 'rb') as handle:
cel_data = StringIO(decompress(handle.read()).decode('ascii'))
Vinc
On 2014-05-18 19:53, Vincent Davis wrote:
> I have a file compressed with bz2 and a function that expects a
> file handle. When I decompress the bz2 file I get a string (binary)
> not a file handle.
> from bz2 import decompress,
>
> with open('Tests/Affy/affy_v3_ex.CEL.bz2', 'rb') as handle:
>
I have a file compressed with bz2 and a function that expects a file handle.
When I decompress the bz2 file I get a string (binary) not a file handle.
Here is what I have that does not work. There is no error (thats a seperate
issue) CelFile.read just fails to read the data(string).
from Bio.Affy
