[Bioperl-l] problem with Bio::SearchIO::Writer

lidaof lidaof at gmail.com
Tue Jan 9 20:37:04 EST 2007


Hi,Dave:

this document also available on CPAN and i have saw it:)
i use a filehandle for output before i know some Text output module such as
Bio::SearchIO::Writer::TextResultWriter or other module
so which variables could be visited by the object created by
Writer::TextResultWriter module?
i have seen no FILE option of the synopsis of TextResultWriter
that is exactly i confusing with
Thank you very much for the advice and information you provided.

Li


On 1/10/07, David Messina <dmessina at wustl.edu> wrote:
>
> > i am confusing with the output of the blast result
> > i use Bio::SearchIO to analysis the blast result
>
> Okay, so you've got the first part.
>
> When you get stuck, the easiest way to learn how to use BioPerl is to
> read the How-Tos:
> http://www.bioperl.org/wiki/HOWTOs
>
> If there is a Hot-To on the topic you're interested in, that is the
> first place you should look.
>
> There is a How-to on SearchIO here:
> http://www.bioperl.org/wiki/HOWTO:SearchIO
>
> Also, lots of questions have already been answered on the mailing
> list. You can search the mailing list archives here:
> http://news.gmane.org/gmane.comp.lang.perl.bio.general
>
>
> > and i don't know how to use Bio::SearchIO::Writer to output the
> > result i
> > want as a Text file
>
> > the document of Bio::SearchIO::Writer is too simple to me
>
> If you go to the documentation for Bio::SearchIO::Writer...
> http://doc.bioperl.org/releases/bioperl-1.5.2/Bio/SearchIO/Writer/
> toc.html
>
> ...you'll see a list of output writers, including
> Bio::SearchIO::Writer::TextResultWriter:
> http://doc.bioperl.org/releases/bioperl-1.5.2/Bio/SearchIO/Writer/
> TextResultWriter.html
>
>
> > can anyone show me some examples for output blast result as text
> > file using
> > Bio::SearchIO::Writer or other Module?
>
> Looking on that page, the synopsis shows this example...
>
>   use Bio::SearchIO;
>   use Bio::SearchIO::Writer::TextResultWriter;
>
>   my $in = new Bio::SearchIO(-format => 'blast',
>                             -file   => shift @ARGV);
>
>   my $writer = new Bio::SearchIO::Writer::TextResultWriter();
>   my $out = new Bio::SearchIO(-writer => $writer);
>   $out->write_result($in->next_result);
>
>
> ...which I think will do exactly what you want.
>
>
> Dave
>



-- 
Li


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