[Biopython-dev] Errors about installing biopython 1.61

[林行众]

Hi Peter
I copy the test_Clustalw_tool.py from the github, now it does work. Thank
you!
Lin

2013/5/13 Peter Cock <p.j.a.cock at googlemail.com>

> 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
>