[Biopython-dev] Errors about installing biopython 1.61

[Peter Cock]

On Mon, May 13, 2013 at 3:34 PM, 林行众 <linxzh1989 at gmail.com> wrote:
>
> Hi Peter
> I have run the locale in my serve
>
> $ locale
> LANG=en_US.UTF-8
> LC_CTYPE=zh_CN.UTF-8
> LC_NUMERIC=zh_CN.UTF-8
> LC_TIME=zh_CN.UTF-8
> LC_COLLATE="en_US.UTF-8"
> LC_MONETARY=zh_CN.UTF-8
> LC_MESSAGES="en_US.UTF-8"
> LC_PAPER=zh_CN.UTF-8
> LC_NAME=zh_CN.UTF-8
> LC_ADDRESS=zh_CN.UTF-8
> LC_TELEPHONE=zh_CN.UTF-8
> LC_MEASUREMENT=zh_CN.UTF-8
> LC_IDENTIFICATION=zh_CN.UTF-8
> LC_ALL=
>
> Is that locale you want?

Hi Lin,

Thanks for checking that, but having looked in more detail
I think this is not related to the locale settings. My first guess
was wrong :(

I think I may have solved this - my test machine has both
clustalw 2.1 and clustalw 1.83, and they behave differently
for this example. The old test only worked with v2.1, fixed:
https://github.com/biopython/biopython/commit/859d07f3c5e8b789156a5ec2e98f4153ab896e00

If you want to verify this, you could update your copy of
Tests/test_Clustalw_tool.py to that from github (or just
tried installing the latest Biopython code from github?).

Note the Clustal developers intended that clustalw 1 and 2
would behave the same as each other (Version 2 was a
rewrite as a step towards version 3, no called ClustalOmega),
but there are still some minor differences.

> I retryed the the test_Entrez_online.py, it's all right now. As
> you said, it should be a connection problem.

OK, good.

> I have put the file in the Doc/examples file, but the error still exists.
> And i find there is no my_blat.psl in Doc/examples comparing with the zip
> file i downloaded from github. After i put the my_blat.psi in the
> Doc/examples, the error did not show up again.

Thank you, that should be fixed in the next release:
https://github.com/biopython/biopython/commit/a3bb49b56abb5cbb9a0a00accb57674115c7004d

Your feedback has been very helpful,

Thanks,

Peter