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

[Sharvari Gujja]

Toshiaki Katayama wrote:
> Hi,
>
> On 2008/01/09, at 10:56, Toshiaki Katayama wrote:
>   
>> 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.
>>     
>
> This was due to the change of the entry name in Swiss-Prot as described at
>
>   http://www.expasy.org/cgi-bin/idtracker?id=ALK1_HUMAN
>
>   
>> The ID: ALK1_HUMAN is no longer valid.
>>
>> ALK1_HUMAN (associated with primary accession number: P03973 from release 9.0) was renamed to SLPI_HUMAN in release 52.0.
>>
>> ALK1_HUMAN was associated with 1 accession number: P07757 from release 12.0.
>>
>> P07757 is now a secondary accession number of SLPI_HUMAN (primary accession number: P03973).
>>     
>
> So, when I specify the USAs as 'uniprot:slpi_human' and 'uniprot:slpi_mouse'
> instead of 'uniprot:alk1_human' and 'uniprot:alk1_mouse',
> I could obtain the proper result.
>
> Toshiaki
>
>
> 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:0x1974d38 @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> hash = {
> bioruby+ "tool" => "water",
> bioruby+ "asequence" => "uniprot:slpi_human",
> bioruby+ "bsequence" => "uniprot:slpi_mouse",
> bioruby+ "email" => "ebisoap at example.org"
> }
>   ==> {"asequence"=>"uniprot:slpi_human", "tool"=>"water", "bsequence"=>"uniprot
> :slpi_mouse", "email"=>"ebisoap at example.org"}
> bioruby> poll = emboss.run(hash, [])
>   ==> "emboss-20080109-01550394"
> bioruby> emboss.checkStatus(poll)
>   ==> "DONE"
> bioruby> base = emboss.poll(poll, "tooloutput")
>   ==> "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!
>  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"
> bioruby> require 'base64'
>   ==> true
> bioruby> puts Base64.decode64(base)
> ########################################
> # Program:  water
> # Rundate:  Wed Jan 09 01:55:06 2008
> # Align_format: srspair
> # Report_file: /ebi/extserv/old-work/emboss-20080109-01550394.output
> ########################################
>
> #=======================================
> #
> # Aligned_sequences: 2
> # 1: SLPI_HUMAN
> # 2: SLPI_MOUSE
> # Matrix: EBLOSUM62
> # Gap_penalty: 10.0
> # Extend_penalty: 0.5
> #
> # Length: 132
> # Identity:      79/132 (59.8%)
> # Similarity:    96/132 (72.7%)
> # Gaps:           3/132 ( 2.3%)
> # Score: 464.5
> # 
> #
> #=======================================
>
> SLPI_HUMAN         1 MKSSGLFPFLVLLALGTLAPWAVEGSGK--SFKAGVCPPKKSAQCLRYKK     48
>                      |||.||.||.||||||.||||.||| ||  :.|.|.||.||.||||:.:|
> SLPI_MOUSE         1 MKSCGLLPFTVLLALGILAPWTVEG-GKNDAIKIGACPAKKPAQCLKLEK     49
>
> SLPI_HUMAN        49 PECQSDWQCPGKKRCCPDTCGIKCLDPVDTPNPTRRKPGKCPVTYGQCLM     98
>                      |:|::||:||||:|||.|.||.||::||....|..||||:|..|..:|:|
> SLPI_MOUSE        50 PQCRTDWECPGKQRCCQDACGSKCVNPVPIRKPVWRKPGRCVKTQARCMM     99
>
> SLPI_HUMAN        99 LNPPNFCEMDGQCKRDLKCCMGMCGKSCVSPV    130
>                      |||||.|:.||||....|||.|:|||.|:.|:
> SLPI_MOUSE       100 LNPPNVCQRDGQCDGKYKCCEGICGKVCLPPM    131
>
>
> #---------------------------------------
> #---------------------------------------
>   ==> nil
>
>
>
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>   

Hi,

How can I use fasta files from NCBI as input to asequence and bsequence?

For examples , I have 2 fasta files BA000002.fasta and CP000030.fasta

Thanks
-S