[Biopython] Planning Biopython 1.72

[Peter Cock]

Hi Martin,

Can you open an issue on this please.

My feeling is a strong negative one - filenames are fragile.
However, when given a filename and we own the handle
and can therefore seek or reopen it as needed, I would
be more neutral on sniffing the filetype instead. If we are
going to do it, we should do it centrally for Bio.SeqIO,
Bio.AlignIO and Bio.SearchIO in one place - but I don't
want to rush that given my intended time frame for getting
Biopython 1.72 out before GCC BOSC 2018.

Thanks,

Peter

On Tue, Jun 12, 2018 at 6:04 PM, Martin Mokrejs
<mmokrejs at fold.natur.cuni.cz> wrote:
> Hi,
>   I just realized that SearchIO does not automatically
> detect compressed files on its input using file extension.
> Could .gz, .bz2 be supported?
>
>>>> for record in SearchIO.parse('blah.xml.gz', 'blast-xml'):
> ...     print record.id
> ...
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File "/usr/lib64/python2.7/site-packages/Bio/SearchIO/__init__.py", line 312, in parse
>     generator = iterator(source_file, **kwargs)
>   File "/usr/lib64/python2.7/site-packages/Bio/SearchIO/BlastIO/blast_xml.py", line 211, in __init__
>     self._meta, self._fallback = self._parse_preamble()
>   File "/usr/lib64/python2.7/site-packages/Bio/SearchIO/BlastIO/blast_xml.py", line 225, in _parse_preamble
>     for event, elem in self.xml_iter:
>   File "<string>", line 91, in next
> cElementTree.ParseError: not well-formed (invalid token): line 1, column 0
>>>>
>
> Martin