[Bioperl-l] using LargeSeq objects

Brian Osborne brian_osborne at cognia.com
Mon Jun 23 12:31:58 EDT 2003


>Go: perldoc Bio::DB::Fasta. I haven't been able to locate the
>documentation on the website.

There's some documentation in the bptutorial
(http://bioperl.org/Core/Latest/bptutorial.html), one question in the FAQ
(http://bioperl.org/Core/Latest/FAQ.html), and some discussion in
biodatabases.pod (http://bioperl.org/Core/Latest/biodatabases.html). There's
also doc/howto/ FLAT-DATABASES-HOWTO.txt, which addresses Bio::DB::Flat in
the context of OBDA. Even bpindex.PLS and bpfetch.PLS have useful
documentation! Certainly scattered, that's not good. Perhaps I should I
write a HOWTO...

One thing we may consider, since we now have 3 systems for local file
indexing, is removing at least one of the 3. Does anyone have any opinions
on this? In the words of Lincoln, this is particularly "weedy". I'd be happy
to write this HOWTO if we take steps towards consolidation. The first step
would be marking something for future deprecation.

Brian O.

-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Morten Lindow
Sent: Monday, June 23, 2003 11:05 AM
To: Michael R Olson
Cc: bioperl-l at portal.open-bio.org
Subject: Re: [Bioperl-l] using LargeSeq objects

Michael R Olson wrote:

>I'm currently writing a program that runs BLAST, then gets the start and
>stop base pairs of the alignment for a hit and goes to the database
>BLAST was run against, and gets base pairs before and after the start
>and stop.  Right now I use LargeSeq objects to read the entire database
>into memory (or a chunk, if it's divided up) and then say
>$str = $seq->subseq($start,$end);
Remember that the exact start and stop depends on the parameter setting
for blast - falloff etc.

>Is this significantly less efficient than going into the database myself
>and using seek, tell and read, because using SeqIO objects is much
>easier, but right now it's very slow.
Use Bio::DB::Fasta - it is very fast and just as convenient.

Go: perldoc Bio::DB::Fasta. I haven't been able to locate the
documentation on the website.

 - Morten

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