Re: Unicode and encoding experts? Sch äffer in BLAST XML

I'm not sure if this is the issue, but could you try specifying the
encoding directly? LANG=C doesn't do anything on my machine, so I can't
reproduce the error and test this myself.

LANG=C python3.5 -c "h = open('xml_2218_blastp_002.xml', encoding='utf-8');
print(h.read(400))"

Thanks,
Shyam

On Mon, Jun 20, 2016 at 6:51 AM, Peter Cock <[email protected]>
wrote:

> Hello all,
>
> Do any of you have first hand experience of unicode encoding
> issues with XML parsing? I'm hoping for some help with this issue:
>
> UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position
> 313: ordinal not in range(128)
>
> https://github.com/biopython/biopython/issues/855
>
> I believe this problem stems from how Alejandro Schäffer is
> *sometimes* written in the BLAST XML output:
>
> https://github.com/biopython/biopython/issues/855#issuecomment-226276235
>
> Thanks,
>
> Peter
>
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