Class: Bio::DDBJ::XML::Blast

Inherits:
Bio::DDBJ::XML show all
Defined in:
lib/bio/io/ddbjxml.rb

Overview

Description

DDBJ XML BLAST Database Search

Examples

serv = Bio::DDBJ::XML::Blast.new
program = 'blastp'
database = 'SWISS'
query = "MSSRIARALALVVTLLHLTRLALSTCPAACHCPLEAPKCAPGVGLVRDGCGCCKVCAKQL"

report = serv.searchSimple(program, database, query)
Bio::Blast::Default::Report.new(report).each_hit do |hit|
  hit.hsps.find_all {|x| x.evalue < 0.1 }.each do |hsp|
    p [hsps.evalue, hsps.identity, hsps.definition]
  end
end

program = 'tblastn'
database = 'ddbjvrl'
param = '-m 8 -e 0.001'
puts serv.searchParam(program, database, query, param)

WSDL Methods

  • searchSimple(program, database, query)

Returns a blast report in the default format.

  • searchParam(program, database, query, param)

Blasts with param and returns a blast report.

References

Constant Summary collapse

SERVER_URI = 
BASE_URI + "Blast.wsdl"

Constants inherited from Bio::DDBJ::XML

BASE_URI

Instance Attribute Summary

Attributes inherited from SOAPWSDL

#log, #wsdl

Method Summary

Methods inherited from Bio::DDBJ::XML

#initialize

Methods inherited from SOAPWSDL

#initialize, #list_methods

Constructor Details

This class inherits a constructor from Bio::DDBJ::XML

Dynamic Method Handling

This class handles dynamic methods through the method_missing method in the class Bio::SOAPWSDL