[BioRuby] bio::blast::reports

[Naohisa GOTO]

On Mon, 8 Dec 2008 09:49:23 +0300
"George Githinji" <georgkam at gmail.com> wrote:

> Hi all
> Using bio 1.2.1 with ruby 1.8.6 on ubuntu 8.01 the following code seems not
> to print anything.
> just wondering why.
> 
> require 'rubygems'
> require 'bio'
> 
> report_file = "/home/george/esther_blast_files/blast_output2.txt"
> Bio::Blast.reports(report_file) do |report|
>   puts report.class
>   puts "am going away"
> end
> 
> report_file is a valid blast report file in m0 format.

Please see document of Bio::Blast.reports.
http://bioruby.rubyforge.org/classes/Bio/Blast.html#M000732
It says "only for xml format".

For default (-m 0) format, Bio::FlatFile.open(filename)
can be used.


Naohisa Goto
ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org