[Bioperl-l] Fwd: SimpleAlign bug?

Chris Fields cjfields at uiuc.edu
Wed Apr 11 08:33:42 EDT 2007


Don't know when this was added.  Maybe we should make the sorting  
optional?  In other words, pass an optional 'nosort' string as the  
first arg, defaulting to numerical sort.

Either way the sort needs to be changed by the looks of it.  I'll  
verify the bug and commit today.

chris

On Apr 11, 2007, at 4:14 AM, Heikki Lehvaslaiho wrote:

> What is going on here? Can anyone remember doing this?
>
> 	-Heikki
>
> Please can I ask what is the purpose of the line @pos = sort @pos; in
> the select_noncont subroutine of SimpleAlign.pm.
>
>
>
> In previous versions this line was not present and I could use the
> function to reorder the alignment e.g in an alignment with 5  
> sequences I
> could reorder it to put the second sequence last using
> $aln->select_noncont(1,3,4,5,2). The sort function stops this, but  
> even
> if the idea is to sort numerically this dos not work since the sort
> function as is will put 10 before 2, so that
> ->select_noncont(1,2,3,4,5,6,7,8,9,10) would reorder the sequences in
> the alignment to be 1, 10, 2, 3, 4,5, 6, 7, 8,9 .
>
>
>
> Many thanks
>
>
>
> Anthony
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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