[Bioperl-l] Fwd: SimpleAlign bug?

Heikki Lehvaslaiho heikki at sanbi.ac.za
Wed Apr 11 05:14:27 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 .


Many thanks



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