[BioRuby] bio::blast::reports

[Toshiaki Katayama]

Goto-san,

Is it impossible to make Bio::Blast.reports understand -m 0 format?

Toshiaki

On 2008/12/08, at 16:51, Naohisa GOTO wrote:

> 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
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