[Bioperl-l] Error parsing blast results with blasttable

[Marc Logghe]

> while (my $result = $searchio->next_result) {
>         while(my $hit = $result->next_hit) {
>                 my $start  = $hit->start;
> 
> And it is that call to $hit->start that sets off the whole trace.
> 
> Any ideas?


Hi Mick,
Have you tried one of these ?:

my $start = $hit->start('sbjct');  # or 'query' or 'hit'. Latter is same as 'sbjct'

or 

my $start = $hit->hsp->start('sbjct');


I think in all cases it defaults to 'query'. So it should not crash but give you the start position of the query.
I am afraid I can't explain the crash, sorry.

Marc