[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.

chris

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
>
>
> ---------------------------------------------------------------------
>
> SECURITY/CONFIDENTIALITY WARNING:
> This message and any attachments are intended solely for the  
> individual or entity to which they are addressed. This communication  
> may contain information that is privileged, confidential, or exempt  
> from disclosure under applicable law (e.g., personal health  
> information, research data, financial information). Because this e- 
> mail has been sent without encryption, individuals other than the  
> intended recipient may be able to view the information, forward it  
> to others or tamper with the information without the knowledge or  
> consent of the sender. If you are not the intended recipient, or the  
> employee or person responsible for delivering the message to the  
> intended recipient, any dissemination, distribution or copying of  
> the communication is strictly prohibited. If you received the  
> communication in error, please notify the sender immediately by  
> replying to this message and deleting the message and any  
> accompanying files from your system. If, due to the security risks,  
> you do not wi!
> sh to receive further communications via e-mail, please reply to  
> this message and inform the sender that you do not wish to receive  
> further e-mail from the sender.
>
> ---------------------------------------------------------------------
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Marie-Claude Hofmann
College of Veterinary Medicine
University of Illinois Urbana-Champaign






More information about the Bioperl-l mailing list