[Bioperl-l] SearchIO: write/read database

Chris Fields cjfields at uiuc.edu
Tue May 20 13:40:30 EDT 2008

Jason has a starter script available in scripts/graphics/ 
search_overview.PLS (should be installed as bp_search_overview.pl if  
you elected to install scripts).  It can draw a simple graphical  
search overview using Bio::Search objects; might be worth a look.


On May 20, 2008, at 12:22 PM, Chu, Roy wrote:

> I've never really explored using pipes beyond the shell envrionment  
> and
> writing images w/ the bioperl GD module but always a good time to  
> learn!
> If I can't get it to work, then I'll just parse the xml output.
> Thanks,
> -Roy
> ________________________________
> From: dave at davemessina.com [mailto:dave at davemessina.com] On Behalf Of
> Dave Messina
> Sent: Tuesday, May 20, 2008 10:10 AM
> To: Chu, Roy
> Cc: Sendu Bala; bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] SearchIO: write/read database
> Echoing what Sendu said, the most straightforward way to read output
> from a program without writing to a file first is to open a pipe from
> the program as a filehandle.
> e.g.
> my @args = ('/usr/bin/blastp', '/path/to/my/blastdb',
> '/path/to/my/blastquery');
> open (my $blast_fh, '-|', @args) or die "couldn't open blast stream";
> Now you can use that filehandle to read in data and manipulate just as
> if you had read it in from a file (except of course since it's a  
> stream
> you can't rewind).
> Dave
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign

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