[BioPython] too lazy to install InterProScan on my computer

[Iddo Friedberg]

Ann,

Just a general comment from one who has recently installed InterProScan 
on his workstation for the first time:

1) Installation is truly a breeze. If you want to mass use interproscan, 
you should do it on your machine. You'll be happier down the road. So 
will EBI: I believe there is a reason they moved from 6 sequences at a 
time to 1 at a time in their web interface.

2) Having said that, I have a Python client that queries InterProScan 
and parses the results. I can give you the code if you like. Not ZSI, 
just plain hacking.

Cheers,

Iddo



Ann Loraine wrote:
> Greetings all,
> 
> I've been trying to get EBI's InterProScan Web service to work with
> ZSI, which I understand  is the preferred SOAP messaging
> implementation for python. I haven't had much luck so far .. I've get
> an error that look like an incompatibility in the WSDL of EBI
> (http://www.ebi.ac.uk/Tools/webservices/wsdl/WSInterProScan.wsdl) and
> what ZSI expects (see below.)
> 
> Has anyone on the list used EBI's InterProScan from python using ZSI?
> If yes, did it work for you?
> 
> Any sample code would be much appreciated, as I am new to SOAP. (EBI
> provides some example perl and java client code, but I'd like to take
> advantage of python's interpreter, which in theory would allow me to
> submit a bunch of requests to EBI using the asynchronous option,
> collect the job ids in a dictionary, and then fetch the data later on
> in the same interactive session.)
> 
> -Ann
> 
> import ZSI
> ebi_wsdl = 'http://www.ebi.ac.uk/Tools/webservices/wsdl/WSInterProScan.wsdl'
>>>> service = ZSI.ServiceProxy(ebi_wsdl)
> Traceback (most recent call last):
>   File "<stdin>", line 1, in ?
>   File "/usr/local/lib/python2.4/site-packages/ZSI/ServiceProxy.py",
> line 34, in __init__
>     wsdl = ZSI.wstools.WSDLTools.WSDLReader().loadFromURL(wsdl)
>   File "/usr/local/lib/python2.4/site-packages/ZSI/wstools/WSDLTools.py",
> line 42, in loadFromURL
>     wsdl.load(document)
>   File "/usr/local/lib/python2.4/site-packages/ZSI/wstools/WSDLTools.py",
> line 260, in load
>     schema = reader.loadFromNode(WSDLToolsAdapter(self), item)
>   File "/usr/local/lib/python2.4/site-packages/ZSI/wstools/XMLSchema.py",
> line 80, in loadFromNode
>     schema.load(reader)
>   File "/usr/local/lib/python2.4/site-packages/ZSI/wstools/XMLSchema.py",
> line 1116, in load
>     tp.fromDom(node)
>   File "/usr/local/lib/python2.4/site-packages/ZSI/wstools/XMLSchema.py",
> line 2283, in fromDom
>     self.content.fromDom(contents[indx])
>   File "/usr/local/lib/python2.4/site-packages/ZSI/wstools/XMLSchema.py",
> line 1996, in fromDom
>     content[-1].fromDom(i)
>   File "/usr/local/lib/python2.4/site-packages/ZSI/wstools/XMLSchema.py",
> line 1764, in fromDom
>     self.setAttributes(node)
>   File "/usr/local/lib/python2.4/site-packages/ZSI/wstools/XMLSchema.py",
> line 627, in setAttributes
>     self.__checkAttributes()
>   File "/usr/local/lib/python2.4/site-packages/ZSI/wstools/XMLSchema.py",
> line 673, in __checkAttributes
>     raise SchemaError,\
> ZSI.wstools.XMLSchema.SchemaError: class instance
> ZSI.wstools.XMLSchema.LocalElementDeclaration, missing required
> attribute name
> 
> 
> 
> 


-- 
Iddo Friedberg, Ph.D.
Burnham Institute for Medical Research
10901 N. Torrey Pines Rd.
La Jolla, CA 92037, USA
T: +1 858 646 3100 x3516
http://iddo-friedberg.org
http://BioFunctionPrediction.org