[Bioperl-l] something wrong with my code?

[Jason Stajich]

Looks like a bug alright, but it has to do with this part of the
alignment in your report.

Query: 301  tccgcctccaccgcctcctcggcaaccggt---------------------------ggt 333
            ||||||||||||||||||||||||||||||                           |||
Sbjct: 8126 tccgcctccaccgcctcctcggcaaccggtaagca<--[8161:8243]-->taggtggt 8251

We currently can't parse that an turn it into anything appropriate - does
it mean there is a gap there or should those bases be 'N's?

Can you report it to http://bugzilla.open-bio.org for the time being.

-jason
On Thu, 2 Oct 2003, Ambrose Ng wrote:

> my code here:
>
> my @s_ind = $hsp->seq_inds('hit', 'id', 1);
> print "conserved=", my $s_ind = join (" ", at s_ind), "\n";
>
> reports this:
>
> conserved=7896-8225 8249-8949
>
>
> but the numbers are different from the blast report.
>
> Is it more likely to do with my code or is there something going on with the
> bioperl module compatibility with this blast report that I'm
> misunderstanding?
>
> Ambrose
>
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu