[Bioperl-l] Fwd: SimpleAlign bug?

Kevin Brown Kevin.M.Brown at asu.edu
Wed Apr 11 11:14:07 EDT 2007

> 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 .

Not sure why 10 would come before 2 since perl would interpret that list
as a series of integers even if they were entered as strings and do the

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