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

David Messina dmessina at wustl.edu
Wed Jan 10 10:58:50 EST 2007


> this document also available on CPAN and i have saw it:)

That's good, but you may want to become familiar with the BioPerl  
website, because the information there is more extensive and more up- 
to-date.


> 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'm not exactly sure what you're asking here. Do you want to know  
what methods can be used on a TextResultWriter object?


> i have seen no FILE option of the synopsis of TextResultWriter

Ahh, that is because TextResultWriter doesn't have a file option. :)
If you look carefully at the example, it is actually Bio::SearchIO  
that take the -file parameter:


>   my $in = new Bio::SearchIO(-format => 'blast',
>                             -file   => shift @ARGV);


This example might be a little confusing because it uses an unusual  
(antiquated?) syntax.
This would do the same thing:

my $in = Bio::SearchIO->new(-format => 'blast',
								 -file => shift @ARGV);

The Bio::SearchIO documentation for the new() method describes all of  
the parameters it can take:

http://doc.bioperl.org/bioperl-live/Bio/SearchIO.html#POD1


> that is exactly i confusing with

BioPerl can be hard to understand at first. Time spent reading  
bioperl.org and this mailing list is a good way to become familiar  
with the "Bioperl way" of doing things.


Dave


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