Bioperl-guts: Batch Entrez via DB::GenBank/GenPept

Aaron J Mackey ajm6q@virginia.edu
Thu, 18 Mar 1999 15:17:38 -0500 (EST)


You can now get_Stream_by_batch($var) where $var can be a filename,
filehandle, or array reference, any of which contain a list of ID's.  This
is a much nicer interface to Entrez, in that their server only get's hit
once (as opposed to get_Stream_by_id/acc() which actually hits it once for
every id in the array ref).  The Batch Entrez interface can be used to
obtain organism-specific sequences as well, if anyone thinks we want this
I can throw it in as well:

$AllMiceSeqsInGenBank = get_Stream_by_organism("mus musculus");

The DB.t test seems to work okay now (although I don't have access to a
machine that has perl that doesn't have internet access to check the
warnings).

I have some beginning FASTA result objects in the works, I'll post some
stuff later ...

-Aaron

-- 
 o ~   ~   ~   ~   ~   ~  o
/ Aaron J Mackey           \
\  Dr. Pearson Laboratory  / 
 \ University of Virginia  \     
 /  (804) 924-2821          \
 \  amackey@virginia.edu    /
  o ~   ~   ~   ~   ~   ~  o


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