[BioRuby] Error running standalone blast

[Ben Woodcroft]

Hi,

I've run into this bug as well and managed to fix it - it is related to a
problematic security fix for Debian and Ubuntu. See

http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=502535
or
https://bugs.launchpad.net/ubuntu/+source/ruby1.8/+bug/291893

Thanks,
ben

2009/3/23 Kevin English <kenglish at gmail.com>

> Hello all,
>  New to bioRuby.
> Following the example I found here:
>
> http://biorelated.wordpress.com/2007/10/03/standalone-blast-with-ruby-part-1
> ,
> I wrote the following program to run a standalone blast. I am getting an
> exception related to rexml... Does anyone know if there is a fix for this?
>
>
> #!/usr/bin/ruby
>
> require 'rubygems'
> require 'bio'
>
> factory = Bio::Blast.local('blastn', '/home/kenglish/Data/EST_B')
> ff = Bio::FlatFile.open(Bio::FastaFormat,
> '/home/kenglish/Data/EST_A.fasta')
>
> ff.each do |entry|
>   puts "Searching..." + entry.definition
>   report = factory.query(entry)
>   report.each do |hit|
>     hit.each do |hsp|
>       puts hsp.query_from
>     end
>   end
> end
>
>
> /usr/lib/ruby/1.8/rexml/entity.rb:76:in `unnormalized': undefined method
> `record_entity_expansion' for nil:NilClass (NoMethodError)
>    from /usr/lib/ruby/1.8/rexml/doctype.rb:135:in `entity'
>    from /usr/lib/ruby/1.8/rexml/text.rb:325:in `unnormalize'
>    from /usr/lib/ruby/1.8/rexml/text.rb:323:in `each'
>    from /usr/lib/ruby/1.8/rexml/text.rb:323:in `unnormalize'
>    from /usr/lib/ruby/1.8/rexml/text.rb:174:in `value'
>    from /usr/lib/ruby/1.8/rexml/element.rb:452:in `text'
>    from /usr/lib/ruby/1.8/rexml/element.rb:433:in `has_text?'
>    from /usr/lib/ruby/1.8/rexml/element.rb:384:in `each_element_with_text'
>    from /usr/lib/ruby/1.8/rexml/element.rb:710:in `call'
>    from /usr/lib/ruby/1.8/rexml/element.rb:710:in `each_with_something'
>    from /usr/lib/ruby/1.8/rexml/element.rb:892:in `each'
>    from /usr/lib/ruby/1.8/rexml/xpath.rb:53:in `each'
>    from /usr/lib/ruby/1.8/rexml/element.rb:892:in `each'
>    from /usr/lib/ruby/1.8/rexml/element.rb:709:in `each_with_something'
>    from /usr/lib/ruby/1.8/rexml/element.rb:388:in `each_element_with_text'
>    from
> /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast/rexml.rb:35:in
> `rexml_parse_program'
>    from
> /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast/rexml.rb:27:in
> `rexml_parse'
>    from
> /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast/report.rb:70:in
> `auto_parse'
>    from
> /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast/report.rb:96:in
> `initialize'
>    from /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast.rb:452:in
> `new'
>    from /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast.rb:452:in
> `parse_result'
>    from /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/appl/blast.rb:370:in
> `query'
>    from blast1.rb:11
>    from /usr/lib/ruby/gems/1.8/gems/bio-1.3.0/lib/bio/io/flatfile.rb:336:in
> `each'
>    from blast1.rb:9
>
> Thanks in advance for any help...
>
> Kevin English
> _______________________________________________
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> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby
>



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