[Biopython-dev] Unicode and encoding experts? Schäffer in BLAST XML

Shyam Saladi saladi at caltech.edu
Mon Jun 20 17:17:01 UTC 2016

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');


On Mon, Jun 20, 2016 at 6:51 AM, Peter Cock <p.j.a.cock at googlemail.com>

> 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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