[BioRuby] help wtih bioruby wrapper for emboss tools...

[Toshiaki Katayama]

Sharvari,

Please write back to the mailing list.

> bioruby> puts Bio::EMBOSS.new("water -asequence 'swissprot:slpi_human' -bsequence 'swissprot:slpi_mouse'").exec
> sh: water: command not found

You need to install EMBOSS suites in your local environment.

> bioruby> emboss = Bio::EBI::SOAP::Emboss.new
> NameError: uninitialized constant Bio::EBI

Use BioRuby 1.2.1 instead of 1.0.0.

> Also where can I find documentation to use other tools in Emboss?

Consult the EMBOSS manual.

Toshiaki


On 2008/01/09, at 23:39, Sharvari Gujja wrote:

> Toshiaki Katayama wrote:
>> Hi Sharvari,
>>
>> What version of the BioRuby are you using?
>>
>> When I tried interactively, SOAP query to EBI was successfully submitted.
>>
>> ------------------------------------------------------------
>> ktym at toge9064:~% bioruby
>> Loading config (/Users/ktym/.bioruby/shell/session/config) ... done
>> Loading object (/Users/ktym/.bioruby/shell/session/object) ... done
>> Loading history (/Users/ktym/.bioruby/shell/session/history) ... done
>>
>> . . . B i o R u b y   i n   t h e   s h e l l . . .
>>
>>  Version : BioRuby 1.2.1 / Ruby 1.8.6
>>
>> bioruby> emboss = Bio::EBI::SOAP::Emboss.new
>> ignored attr: {}nillable
>>  ==> #<Bio::EBI::SOAP::Emboss:0x1978dd4 @driver=#<SOAP::RPC::Driver:#<SOAP::RPC::Proxy:http://www.ebi.ac.uk/cgi-bin/webservices/WSEmboss>>, @log=nil, @wsdl="http://www.ebi.ac.uk/Tools/webservices/wsdl/WSEmboss.wsdl">
>> bioruby> emboss.list_methods
>>  ==> ["run", "checkStatus", "getResults", "getTools", "poll", "getInfo"]
>> bioruby> hash = {
>> bioruby+ "tool" => "water",
>> bioruby+ "asequence" => "uniprot:alk1_human",
>> bioruby+ "bsequence" => "uniprot:alk1_mouse",
>> bioruby+ "email" => "ebisoap at example.org"
>> }
>>  ==> {"asequence"=>"uniprot:alk1_human", "tool"=>"water", "bsequence"=>"uniprot:alk1_mouse", "email"=>"ebisoap at example.org"}
>> bioruby> poll = emboss.run(hash, [])
>>  ==> "emboss-20080108-19402170"
>> bioruby> emboss.checkStatus(poll)
>>  ==> "RUNNING"
>> ------------------------------------------------------------
>>
>> Real problem here is that the EBI server never finishes this work...
>> 5 hours later, the process is still (reported to be) running
>> thus I can't obtain the result yet.
>>
>> ------------------------------------------------------------
>> bioruby> emboss.checkStatus(poll)
>>  ==> "RUNNING"
>> bioruby> base = emboss.poll(poll, "tooloutput")
>>  ==> nil
>> ------------------------------------------------------------
>>
>> Regards,
>> Toshiaki Katayama
>>
>>
>> On 2008/01/09, at 4:03, Sharvari Gujja wrote:
>>
>>  
>>> Hi all,
>>>
>>> I am trying to use emboss tool "water" in bioruby. However when I try to run the following script I get the error as : uninitialized constant Bio::EBI (NameError).
>>>
>>> Do I need to import any files?
>>>
>>> #!/usr/bin/env ruby
>>> require 'bio'
>>> require 'base64'
>>> emboss = Bio::EBI::SOAP::Emboss.new
>>>
>>> emboss.list_methods
>>>
>>> hash = {
>>> "tool" => "water",
>>> "asequence" => "uniprot:alk1_human",
>>> "bsequence" => "uniprot:alk1_mouse",
>>> "email" => "ebisoap at example.org"
>>> }
>>> poll = emboss.run(hash, [])
>>> emboss.checkStatus(poll)
>>> base = emboss.poll(poll, "tooloutput")
>>> puts Base64.decode64(base)
>>>
>>>
>>> Thanks
>>> -S
>>>
>>> _______________________________________________
>>> BioRuby mailing list
>>> BioRuby at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioruby
>>>    
>>
>>
>> _______________________________________________
>> BioRuby mailing list
>> BioRuby at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioruby
>>  
> Hello Mr.Toshiaki,
>
> Thank you for the reply. This is what I get when I do the same:
>
> bioruby:14:Warning: require_gem is obsolete.  Use gem instead.
> Loading config (session/config) ... done
> Loading object (session/object) ... done
> Loading history (session/history) ... done
>
> . . . B i o R u b y   i n   t h e   s h e l l . . .
>
> Version : BioRuby 1.0.0 / Ruby 1.8.6
>
> bioruby> puts Bio::EMBOSS.new("water -asequence 'swissprot:slpi_human' -bsequence 'swissprot:slpi_mouse'").exec
> sh: water: command not found
>
> bioruby> emboss = Bio::EBI::SOAP::Emboss.new
> NameError: uninitialized constant Bio::EBI
>       from (irb):2
>
> I am trying to download the latest version 1.2.0 and I get the tar file.I was wondering how to proceed from there.
>
> Also where can I find documentation to use other tools in Emboss?
>
> I really appreciate your help.
>
> Thanks
> Sharvari