New submission from Peter <p.j.a.c...@googlemail.com>:
Consider the following example where I have a gzipped text file,
$ python3
Python 3.2 (r32:88445, Feb 28 2011, 17:04:33)
[GCC 4.2.1 (Apple Inc. build 5664)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import gzip
>>> with gzip.open("ex1.sam.gz") as handle:
... line = handle.readline()
...
>>> line
b'EAS56_57:6:190:289:82\t69\tchr1\t100\t0\t*\t=\t100\t0\tCTCAAGGTTGTTGCAAGGGGGTCTATGTGAACAAA\t<<<7<<<;<<<<<<<<8;;<7;4<;<;;;;;94<;\tMF:i:192\n'
Notice the file was opened in binary mode ("rb" is the default for gzip.open
which is surprising given "t" is the default for open on Python 3), and a byte
string is returned.
Now try explicitly using non-binary reading "r", and again you get bytes rather
than a (unicode) string as I would expect:
>>> with gzip.open("ex1.sam.gz", "r") as handle:
... line = handle.readline()
...
>>> line
b'EAS56_57:6:190:289:82\t69\tchr1\t100\t0\t*\t=\t100\t0\tCTCAAGGTTGTTGCAAGGGGGTCTATGTGAACAAA\t<<<7<<<;<<<<<<<<8;;<7;4<;<;;;;;94<;\tMF:i:192\n'
Now try and use "t" or "rt" to be even more explicit that text mode is desired,
>>> with gzip.open("ex1.sam.gz", "t") as handle:
... line = handle.readline()
...
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/Users/pjcock/lib/python3.2/gzip.py", line 46, in open
return GzipFile(filename, mode, compresslevel)
File "/Users/pjcock/lib/python3.2/gzip.py", line 157, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
ValueError: can't have text and binary mode at once
>>> with gzip.open("ex1.sam.gz", "rt") as handle:
... line = handle.readline()
...
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/Users/pjcock/lib/python3.2/gzip.py", line 46, in open
return GzipFile(filename, mode, compresslevel)
File "/Users/pjcock/lib/python3.2/gzip.py", line 157, in __init__
fileobj = self.myfileobj = builtins.open(filename, mode or 'rb')
ValueError: can't have text and binary mode at once
See also Issue #5148 which is perhaps somewhat related.
----------
components: None
messages: 153067
nosy: maubp
priority: normal
severity: normal
status: open
title: gzip always returns byte strings, no text mode
versions: Python 3.2
_______________________________________
Python tracker <rep...@bugs.python.org>
<http://bugs.python.org/issue13989>
_______________________________________
_______________________________________________
Python-bugs-list mailing list
Unsubscribe:
http://mail.python.org/mailman/options/python-bugs-list/archive%40mail-archive.com
