How to solve this problem? ruby application.

[alpha2cen]

I used bioruby program before.

But it has some problem.

What is the matter? It dose not work well. I do not know the cause of the trouble.

 

ruby program

[quit]

require 'rubygems'

require 'bio'

 

#if __FILE__ == $0

 

begin

require 'pp'

alias p pp

rescue LoadError

end

 

puts ">>> Bio::DDBJ::XML::Blast"

serv = Bio::DDBJ::XML::Blast.new

# serv.log = STDERR

 

query = "MSSRIARALALVVTLLHLTRLALSTCPAACHCPLEAPKCAPGVGLVRDGCGCCKVCAKQL"

 

puts "### searchSimple('blastp', 'SWISS', query)"

puts serv.searchSimple('blastp', 'SWISS', query)

 

 

 

execution result

 

>>> Bio::DDBJ::XML::Blast

/usr/lib/ruby/1.8/net/http.rb:560:in `initialize': getaddrinfo: Name or service not known (SocketError)

 

When the SocketError occurs?

Edited August 22, 2012 by alpha2cen

[ecoli]

alpha2cen: http://www.statisticalanalysisconsulting.com/how-to-ask-a-statistics-question/ This applies equally well to computational questions as well.

[alpha2cen]

This program work well before. But it does not give query search result any more. When that kind phenomena occurs? What is the socket error? Special question?

[ecoli]

alpha - you have not yet explained what you are trying to do. A quick google search indicates that a socket error could result from a bad connection to whatever server you're using.

[alpha2cen]

I would like to study about searching similar species or similar DNA profile at the Blast DB. Using the bioruby program(gem program) I could do it well before. I used it several times without problem.

So, they block to use the DB(bio DB) against the external user? In that case" Socket Error" message appears?

[ecoli]

found this similar problem on stackoverflow: http://stackoverflow.com/questions/2608331/net-http-rb560in-initialize-getaddrinfo-name-or-service-not-known-sockete

 

 

"Name or service not known" is a socket-level error which usually points to either an invalid IP address/DNS hostname, or an unregistered port name"

 

You might want to post this on a [bio]Ruby thread/forum. If the program isn't connecting BlastDB and you're sure your network connection is fine, perhaps there's some deeper issue/bug. I don't know how many Ruby programmers we have on SFN [i am not one]