[Bioperl-l] problem with Bio::SearchIO::Writer
dmessina at wustl.edu
Tue Jan 9 17:29:42 UTC 2007
> 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...
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.
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