[Biopython-dev] Git master branch freeze for Biopython 1.69 release

[Peter Cock]

On Fri, Apr 7, 2017 at 3:39 PM, Fulton, Ben <befulton at iu.edu> wrote:
> Pull request submitted. Did you just copy that comment from the last release email?  ☺
>

Not consciously, grin.

> I got an error in testing that I don't remember seeing before:
>
> ======================================================================
> ERROR: test_correct_retrieval_1 (test_MafIO_index.TestSpliceGoodMAF)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "C:\Users\befulton\Documents\GIT\biopython\Tests\test_MafIO_index.py", line 398, in test_correct_retrieval_1
>     3227479), 1)
>   File "C:\Users\befulton\Documents\GIT\biopython\build\lib.win32-3.5\Bio\AlignIO\MafIO.py", line 555, in get_spliced
>     fetched = [multiseq for multiseq in self.search(starts, ends)]
>   File "C:\Users\befulton\Documents\GIT\biopython\build\lib.win32-3.5\Bio\AlignIO\MafIO.py", line 555, in <listcomp>
>     fetched = [multiseq for multiseq in self.search(starts, ends)]
>   File "C:\Users\befulton\Documents\GIT\biopython\build\lib.win32-3.5\Bio\AlignIO\MafIO.py", line 530, in search
>     (rec_start, rec_end, offset, start, end))
> ValueError: Expected 3185728-3185798 @ offset 1974167, found 3185634-3185641
>
> I don't know if it's a Windows thing, or known bug, or something else.


That is troubling. Could you log this as an issue on GitHub? Was it
just Python 3.5?

Peter