[BioPython] AlignIO: Sequences of different length

[Peter]

On Thu, Dec 4, 2008 at 6:19 PM, João Rodrigues <anaryin at gmail.com> wrote:
> I believe the script I gave you had the needle function on it :x It's just a
> simple WSDL file provided by EBI being used by the SOAPpy module to access
> the webservice. The parameters are default as well so, gapopen 10.0 and
> gapextend 0.5.

Oh yes - I see it now on pastebin, previously I'd only looked at the
output file.

> The page of the service is:
> http://www.ebi.ac.uk/Tools/webservices/services/emboss
>
> I kind of noticed that non-sense gap, but that comes with the format
> unfortunately. I ran the Web version of the program, not the webservice, and
> the outcome was the same (regarding the gap):
>
> http://www.ebi.ac.uk/Tools/es/cgi-bin/jobresults.cgi/needle/needle-20081204-18180513899973.html
>

So the web versions of EMBOSS are using spaces for leading gaps
(program version unknown), while the standalone version of EMBOSS (up
to version 6.0.1) are using dashes (minus signs).  Biopython 1.49
expects the leading dashes.

I suspect that the EBI are running a more recent not-yet-released
version of the EMBOSS tools to power their webservices.  I'm not
familiar enough with their code to know where to look...

I suggest you email the webservice people and ask them why the needle
output is different to the command line version (tell them parsers
such as Biopython may be broken by this change).

If this is a forthcoming change to the EMBOSS standalone tools, then I
guess we'll have to fix the parser anyway.  I may find time to look at
this over the weekend - we'll see.

Regards,

Peter