[Biopython-dev] Win7 x64 - python 3.4 - Phylo and searchIO

[Peter Cock]

On Tue, Apr 22, 2014 at 10:36 PM, Manlio Calvi <manlio.calvi at gmail.com> wrote:
> I got those two new errors:
>
> ======================================================================
> ERROR: test_unicode_exception (test_Phylo.IOTests)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "C:\Users\Public\BioPython3\biopython\Tests\test_Phylo.py",
> line 57, in test_unicode_exception
>     tree = Phylo.read(EX_NEWICK_BOM, 'newick')
>   File "C:\Users\Public\BioPython3\biopython\build\lib.win-amd64-3.4\Bio\Phylo\_io.py",
> line 65, in read
>     tree = next(tree_gen)
>   File "C:\Users\Public\BioPython3\biopython\build\lib.win-amd64-3.4\Bio\Phylo\_io.py",
> line 53, in parse
>     for tree in getattr(supported_formats[format], 'parse')(fp, **kwargs):
>   File "C:\Users\Public\BioPython3\biopython\build\lib.win-amd64-3.4\Bio\Phylo\NewickIO.py",
> line 107, in parse
>     for line in self.handle:
>   File "C:\Python34\lib\encodings\cp1252.py", line 23, in decode
>     return codecs.charmap_decode(input,self.errors,decoding_table)[0]
> UnicodeDecodeError: 'charmap' codec can't decode byte 0x9d in position
> 15: character maps to <undefined>
>

Yep, see https://github.com/biopython/biopython/issues/311

> ======================================================================
> FAIL: test_xml_2226_blastn_006 (test_SearchIO_blast_xml.BlastXmlSpecialCases)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
>   File "C:\Users\Public\BioPython3\biopython\Tests\test_SearchIO_blast_xml.py",
> line 3127, in test_xml_2226_blastn_006
>     "Expected one BiopythonParserWarning, got %r" % w)
> AssertionError: 2 != 1 : Expected one BiopythonParserWarning, got
> [<warnings.WarningMessage object at 0x000000000BD0FE10>,
> <warnings.WarningMessage object at 0x000000000C0219B0>]
>

I suspect I have seen that before... must double check that.

@Bow, I think this check needs to be relaxed slightly (e.g. at
least one warning?) as it can potentially interact with global
warning settings (even though the test framework tries to
restore the filters to a known state before each test). Could
you take a look?

Thanks,

Peter