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, 201213 yr by alpha2cen

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

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?

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.

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?

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]