[Bioperl-l] Padded position in Consensus sequence

[Jamie Hatfield]

The Bio::LocatableSeq object is good at doing what you're looking for.

#!/usr/local/bin/perl -w
use Bio::LocatableSeq;
my $consensus = "AGG*TGAC**TA***AGTCCT*T";

 ## gaps are represented using '-' instead of '*' in this object.
 ## either way, though, we need a count of the number of gaps.
 ## if your seq already had '-' representing gaps, then
 ## my $gaps = ($consensus =~ s/-/-/g); 
 ## would still work.
my $gaps = ($consensus =~ s/\*/-/g);
my $seq = new Bio::LocatableSeq(-seq => $consensus, 
                                -id => "consensus",
                                -start => 1, 
                                -end => length($consensus)-$gaps);

print map { "$_\t" . $seq->column_from_residue_number($_) . "\n" } 
      ($seq->start..$seq->end);

On Thu, 2003-08-14 at 11:18, Jayaprakash Rudraraju wrote:
> 
> Hi,
> 
> I have written a small subroutine to as part of the program to tag primers
> in Consed. The following subroutine gives padded position on the consensus
> sequence, given its position on reference sequence.
> 
> #!perl -w
> my $consensus = "AGG*TGAC**TA***AGTCCT*T";
> print map { "$_\t". padded_position($_) ."\n"} (1..16);
> 
> sub padded_position {
>     my ($unpad, $pads) = (@_, 0);
>     $pads++ until $unpad == substr($consensus, 0, $unpad+$pads) =~ tr/ACGT//;
>     $unpad+$pads;
> }
> 
> can you suggest me some more efficient or elegant solutions. Eventhough I
> have condensed it as much as I can, I am looking for a simpler logic.
> 
> Prakash.
> 
> --
> My favorite animal is steak.
> -- Fran Lebowitz (1950 - )
> 
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