[Biopython-dev] New BLAST web page

[Jeffrey Chang]

Hi Brad,

Thanks for these fixes.  I've applied the patches and am trying to search
for sequences against the NCBI web site.  Unfortunately, I seem to be only
getting a piece of the results back!  The output cuts off suddenly in the
alignments section.

----------------
[...]
<a name = 3334489></a><a
href="http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=Protein&list_uids=03334489&dopt=GenPept">sp|P15398|RPA1_SCHPO</a>
DNA-DIRECTED RNA POLYMERASE I 190 KDA POLYPEPTIDE
          Length = 1689

 Score = 28.9 bits (63), Expect = 9.0
 Identities = 12/38 (31%), Positives 

------------------

However, the web version seems to be doing the same thing, so it's very
likely not your patches.  Are you seeing the same thing?

I'm going to wait and see if this clears up over the next few days, before
I commit the patch.

Thanks,
Jeff



On Sun, 18 Mar 2001, Brad Chapman wrote:

> Hi Jeff;
> Thanks for helping me out with this! 
> 
> > Looks like our friends at NCBI have changed
> > the BLAST pages again and added a bunch of new options.  Looking at the
> > page source for the CGI page, they seem to have added a bunch of hidden
> > fields that the CGI script isn't happy to be without:
> 
> Oooh tricky, hidden fields. Thanks for the pointer on these, this gave 
> me the push I needed to get by where I was stuck at.
> 
> > This gets it past the first page, and now gets to the page that tells you
> > to wait for the results.  However, it's been on that page for a while, so
> > I don't know if this is completely going to work, or if NCBI is just slow
> > now!
> 
> Well, it didn't completely finish us up, but getting me past getting
> back the same query page was all I needed :-). Quite a few things have 
> changed in parsing the pages. Since they are now using javascript
> (bleah!), some of the information is in new places.
> 
> But, I think I got it all sorted out and have got things
> working. Attached is a patch against the current CVS which seems to
> get NCBIWWW.blast working for me again. If this seems to work good to
> people, I'll be happy to check it in.
> 
> Also included in a patch is a change to the WWW parser. It looks like
> the format has changed yet again -- they now appear to be putting the
> database before the Query=. The new version seems to parse the new
> stuff correctly, and passed all of the tests with the old versions.
> 
> So, with this patch it seems like we work again with NCBI Blast. Whew!
> I hope this works right for everyone else.
> 
> Thanks again for the help, Jeff!
> 
> Brad
> 
>