[ensembl-dev] Question regarding the Variant Effect Predictor script

[Duarte Molha]

Hello

I have been looking at the source code for the variant predictor script and
I have a question regarding a section of the code:

828  else {
829 $ref = substr($ref, 1);
830 $ref = '-' if $ref eq '';
831 $start++;
832
833 foreach my $alt_allele(split /\,/, $alt) {
834 $alt_allele = substr($alt_allele, 1);
835 $alt_allele = '-' if $alt_allele eq '';
836 push @alts, $alt_allele;
837 }
838 }
839
840 $alt = join "/", @alts;

It does not make sense to me that you define $alt_allele as a substring  of
$alt_allele in line 834

Indels can be bigger than 1 bp so why are you doing this?

You do the same for variations that have only 1 alternative allele (line
871):

868 else {
869 # chop off first base
870 $ref = substr($ref, 1);
871 $alt = substr($alt, 1);

Can you explain why this is necessary or indeed correct?

Best regards,

     Duarte Molha

=========================
     Duarte Miguel Paulo Molha
         Tel: +447772111304
  Email: duartemolha at gmail.com
=========================
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20110419/426c9e37/attachment.html>