[Bioperl-l] change in Tools::SeqWords not reflected in tutorial link

[Brian Osborne]

William,

Fixed. Probably the most appropriate place to submit a requested fix like
this is http://bugzilla.bioperl.org/, that way it won't get lost.

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 William Hsiao
Sent: Wednesday, December 03, 2003 2:07 PM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] change in Tools::SeqWords not reflected in tutorial
link

Hi,
       I noticed that the link for Tool::SeqWords documentation from the
tutorial page (http://bioperl.org/Core/Latest/bptutorial.html) is to the
old version of SeqWords which only allows counting of "ATCG" as shown in
the following code

while($seqstring =~ /(([ACGT]){$word_length})/gim)...

       The new version that's distributed with Bioperl 1.2.3 (supposedly
that's the one covered by the tutorial) counts any words (using /w
instead of [ACGT]).  Since there is no checking mechanism for input
sequences, the change can cause drastic effect on the result (especially
when ambiguous nucleotide sequences are involved).  It would be great if
the change can be reflected in the tutorial to avoid confusion.  The
link should be to
(http://doc.bioperl.org/releases/bioperl-1.2.3/Bio/Tools/SeqWords.html).

Thanks

Cheers

Will

William Hsiao
Graduate Student, Brinkman Laboratory
Department of Molecular Biology and Biochemistry
Simon Fraser University, 8888 University Dr.
Burnaby, BC, Canada V5A 1S6
Phone: 604-291-4206 Fax: 604-291-5583



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