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

[Toshiaki Katayama]

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 The ID: ALK1_HUMAN is no longer valid.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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"
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