[Biopython] Biopython 1.60 and ExPASy Swiss-Prot search functions

[Peter Cock]

On Sun, Jan 27, 2013 at 6:28 AM, Cristian Alejandro Rojas Quintero
<alejandro.0317 at gmail.com> wrote:
> Hi all,
>
> I'm trying to make a search of Swiss-Prot records on ExPASy with
> sprot_search_ful and sprot_search_de ,  But appears like the ExPASy server
> has been moved, I tried to read the help from the modules and all that I can
> find is that the cgi url is "http://www.expasy.ch/cgi-bin/sprot-search-ful"
> or "http://www.expasy.ch/cgi-bin/sprot-search-de". I'm trying to access in
> that URLs with my web browser but appears a error message indicating that
> the site to search is www.uniprot.org. Maybe the functions won't work
> anymore because the server has been moved?
>
> Or am I doing something bad?
>
> These are the steps to reproduce the error.
>>>> handle=ExPASy.sprot_search_ful("Insulin")
>>>> print handle.read()
> As you can see the status code for http request was 302. BTW: The release
> date of the new server was jan 9, 2013
>
> Thank you.
> **

It looks like ExPASy have retired some more URLs - they did this
and broke our get_sprot_raw function three years ago:
https://github.com/biopython/biopython/commit/6689bf8657d9515965d63f9c77e6348233472046

If you can work out what the new URLs are this should be easy to fix -
last time they had a table at http://www.expasy.ch/expasy_urls.html
but that page doesn't exist any more :(

In this case, the Error 302 tells us to use:
http://www.uniprot.org/uniprot?query=Insulin&S=on

Would you like to try updating Bio/ExPASy/__init__.py (and
making a pull request on Github)?

Regards,

Peter