[Bioperl-l] Fwd: SimpleAlign bug?

Andreas Kahari ak at ebi.ac.uk
Wed Apr 11 11:58:52 EDT 2007


On Wed, Apr 11, 2007 at 08:14:07AM -0700, Kevin Brown 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 .
> 
> 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
> sort.

Really?

$ perl -e 'print join(" ", sort(1..20)), "\n"';
1 10 11 12 13 14 15 16 17 18 19 2 20 3 4 5 6 7 8 9


-- 
Andreas Kähäri :: Ensembl Software Developer
European Bioinformatics Institute (EMBL-EBI)
-------------------*=<>=*-------------------


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