[BioRuby] bio blast

[George Githinji]

Thank you Nakao for the reply. Removing the M 0 does not get the error off
instead i get this:
[NULL_Caption] ERROR: Arguments must start with '-' (the offending argument
#7 was: 'local')


Which i presume means i have to give an argurments list so i try declaring
the matrix with -M BLOSUM62 and i get this:

C:/ruby-1.8.6/ruby/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/appl/blast/format8.rb:70:in
`tab_parse_hsp': undefined method `strip' for nil:NilClass (NoMethodError)

        from C:/ruby-1.8.6/ruby/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/appl/blast/format8.rb:32:in
`tab_parse'

        from C:/ruby-1.8.6/ruby/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/appl/blast/format8.rb:30:in
`each'

        from C:/ruby-1.8.6/ruby/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/appl/blast/format8.rb:30:in
`tab_parse'

        from C:/ruby-1.8.6/ruby/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/appl/blast/report.rb:71:in
`auto_parse'

        from C:/ruby-1.8.6/ruby/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/appl/blast/report.rb:89:in
`initialize'

        from C:/ruby-1.8.6/ruby/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/appl/blast.rb:232:in
`new'

        from C:/ruby-1.8.6/ruby/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/appl/blast.rb:232:in
`parse_result'

        from C:/ruby-1.8.6/ruby/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/appl/blast.rb:246:in
`exec_local'

        from C:/ruby-1.8.6/ruby/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/appl/blast.rb:212:in
`send'

        from C:/ruby-1.8.6/ruby/lib/ruby/gems/1.8/gems/bio-1.2.1/lib/bio/appl/blast.rb:212:in
`query'

        from F:/Netbeans_folder/vargene/lib/bio_blast.rb:8



On Jan 30, 2008 7:28 PM, Mitsuteru Nakao <n at bioruby.org> wrote:

> Hi
>
> If you remove the options "-m 0", you may get the search result
> without the error.
> # Because I don't have Windows.:-(
>
> > factory = Bio::Blast.new("blastp","#{db}","", "local")
>
>
> And thank you for your bug report.
> this is a bug in the Bio::Blast::Report class.
>
> > factory = Bio::Blast.new("blastp","#{db}","-m  0", "local")
>
>
> hanks.
>
> Mitsuteru,
> -
> Mitsuteru Nakao, Ph.D.
> n at bioruby.org / mn at kazusa.or.jp
>



-- 
---------------
Sincerely
George

Skype: george_g2
Website: http://biorelated.wordpress.com/