[Biopython] Fwd: Bug in bgzf module

[Peter Cock]

On Wed, Jan 30, 2013 at 9:50 PM, Petra Kubincová
<petra.kubincova at gmail.com> wrote:
> Hello,
>
> recently I have installed and tried out biopython 1.60, especially bgzf
> module. I have discovered that calling method "tell()" of object of
> bgzf.BgzfWriter type raises this error:
>
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File "/usr/local/lib/python2.6/dist-packages/Bio/bgzf.py", line 743, in
> tell
>     return make_virtual_offset(self.handle.tell(), len(self._buffer))
> AttributeError: 'BgzfWriter' object has no attribute 'handle'
>
> I've checked out source code of bgzf module. Source code of error-raising
> method "tell()" looks like this:
>
> def tell(self):
>     """Returns a BGZF 64-bit virtual offset."""
>     return make_virtual_offset(self.handle.tell(), len(self._buffer))
>
> The problem is that BgzfWriter does not have variable called "handle", only
> "_handle". So (IMHO) all that needs to be done to fix this bug is change
> "self.handle.tell()" to "self._handle.tell()".
>
> Cheers,
> Petra Kubincova

Hi Petra,

It is nice to know people are using this relatively new code :)

Thank you for pointing that out, that is the correct fix:
https://github.com/biopython/biopython/commit/2a1be2f3e9b731fa05cc4ad7a01a67866155827c

We should add a unit test for this too, in Tests/test_bgzf.py -
is that something you'd like to try and do? If not I'll try to
remember to add something myself.

The reason I implemented the BgzfWriter tell method was for
the use-case of writing a BGZF compressed file while also
recording an index. I'm curious if that's what you are doing,
or if you had another purpose?

Thanks,

Peter