[Bioperl-l] Bio::Root::IO reads URLs from -file

Jason Stajich jason at cgt.duhs.duke.edu
Sun Aug 8 10:30:16 EDT 2004

I'm sort of against putting too much in Root::IO only because it means one
more thing that can go wrong in an essential component.  I'd rather make
the logic explicit so maybe going the -url route would be safer?

The 'longway' for doing this is, below, is this still too much work?  I
guess you want to have the retry in place.

my $bp = Bio::SeqIO->new(-format => 'fasta',
	                 -fh => Bio::Root::HTTPget->getFH($url) );


On Sun, 8 Aug 2004, Allen Day wrote:

> just commited this to cvs.  if you pass a -file arg to a Root::IO
> subclass, the following happens:
> if(the file exists){
>   do as before
> }
> elsif(the file doesn't exist, and the name looks like a url) {
>   try a few times to {
>     download the url to a local tempfile, and update -file to point
>     to the tempfile
>   }
>   if(couldn't download the file){
>     throw an error
>   }
> }
> i'm open to moving urls to a special -url argument instead of overloading
> -file.  what do people think?
> -allen
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Jason Stajich
Duke University
jason at cgt.mc.duke.edu

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