[Bioperl-l] Fwd: SimpleAlign bug?
Kevin.M.Brown at asu.edu
Wed Apr 11 11:14:07 EDT 2007
> What is going on here? Can anyone remember doing this?
> 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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