[Bioperl-l] problem with Bio::SearchIO::Writer
lidaof at gmail.com
Tue Jan 9 20:37:04 EST 2007
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
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.
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:
> 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:
> Also, lots of questions have already been answered on the mailing
> list. You can search the mailing list archives here:
> > 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...
> ...you'll see a list of output writers, including
> > 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);
> ...which I think will do exactly what you want.
More information about the Bioperl-l