Bioperl: Question: reading in blast results from scalar?

[Steve Chervitz]

Note that the documentation to the parse method of the Blast.pm module 
states that the -FILE option should point to a file containing the raw 
Blast output, and if not supplied, STDIN is used. 

This isn't the whole story (yes, the docs need to be updated). 
The -FILE parameter can also contain a FileHandle object or a 
typeglob reference.

Given this, Aaron's suggestion seems like a good one, though I also
have not tested it. 

Steve
--
Steve Chervitz
sac@neomorphic.com

Aaron J Mackey writes:
 > 
 > Another option would be to use the IO::Scalar module to wrap the scalar as
 > a filehandle, and pass that along to the parser (not tested, but can't see
 > why that wouldn't work).
 > 
 > -Aaron
 > 
 > On Tue, 15 Feb 2000, David Block wrote:
 > 
 > > This may be a naive answer, but could you just print the scalar to a file
 > > (or STDOUT) and then pass it along (pipe it)?
 > > 
 > > -Dave
 > > 
 > > On Tue, 15 Feb 2000, Nathan O. Siemers wrote:
 > > 
 > > > 
 > > > Perhaps this is a general perl question.
 > > > 
 > > > 	How does one submit a blast output for parsing, etc, using
 > > > 	Blast.pm, when you have stored the blast result itself into a
 > > > 	scalar, rather than a file?
 > > > 
 > > > 	Thanks,
 > > > 
 > > > 	nathan
 > > > 
 > > > -- 
 > > > N a t h a n   O .  S i e m e r s
 > > > Bioinformatics
 > > > Division of Applied Genomics
 > > > Bristol-Myers Squibb Pharmaceutical Research Institute
 > > > Hopewell Building 3B, P.O. Box 5400, Princeton, NJ 08543-5400
 > > > 609 818-6568
 > > > siemersn@bms.com
 > > > 
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 > -- 
 >  o ~   ~   ~   ~   ~   ~  o
 > / Aaron J Mackey           \
 > \  Dr. Pearson Laboratory  / 
 >  \ University of Virginia  \     
 >  /  (804) 924-2821          \
 >  \  amackey@virginia.edu    /
 >   o ~   ~   ~   ~   ~   ~  o
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