[Bioperl-l] results problem with StandAloneBlast

[Genevieve DeClerck]

Thanks for your comment Sendu, it was very helpful. I think this must be 
what's going on.. I am using $blast_report->next_result in both 
subroutines. It appears that analyzing the blast results first w/ my 
sort subroutine empties (?) the $blast_result object so that when I try 
to print, there is nothing left to print. (and visa-versa when I print 
first then try to sort).
So, from the looks of things, using next_result has the effect of 
popping the Bio::Search::Result::ResultI objects off of the SearchIO 
blast report object??

It seems I could get around this by making a copy of the blast report by 
setting it to another new variable...(not the most elegant solution) but 
I'm having trouble with this...

If I do:

	my $blast_report_copy = $blast_report;

I'm just copying the reference to the SearchIO blast result, so it 
doesn't help me. How can I make another physical copy of this blast 
result object? Seems like a simple thing but how to do it is escaping me.

But better yet, the way to go is to 'reset the counter,' or to find a 
way to look at/print/sort the results without removing data from the 
blast result object. How is this done though??

Sendu and Brian, I didn't post the sort_results subroutine because it is 
sprawling, as is a lot of my code. The code I provided was more like an 
aid for my explanation of the problem.. it doesn't actually run - sorry 
for the confusion, I should have more clear on that.  The important 
thing to know perhaps is that both sort_results and print_blast_results 
contain a foreach loop where I am using the 'next_results' method to 
view blast results. (And to clarify for Torsten, the blastall() is 
working just fine - the analysis/viewing of the results object is where 
I am encountering the problem.)


Any other ideas would be greatly appreciated...

Thank you,
Genevieve




Sendu Bala wrote:

> Genevieve DeClerck wrote:
> 
>> Hi,
> 
> [snip]
> 
>> If I've sorted the results the sorted-results will print to screen, 
>> however when I try to print the Hit Table results nothing is returned, 
>> as if the blast results have evaporated.... and visa versa, if i 
>> comment out the part where i point my sorting subroutine to the blast 
>> results reference,  my hit table results suddenly prints to screen.
> 
> [snip]
> 
>> Here's an abbreviated version of my code:
> 
> [snip]
> 
>> #######
>> ### the following 2 actions seem to be mutually exclusive.
>> # 1) sort results into 1-hitter, 2-hitter, etc. groups of
>> # SeqFeature objs stored in arrays. arrays are then printed
>> # to stdout
>> &sort_results($blast_report);
>>
>> # 2) print blast results
>> &print_blast_results($blast_report);
> 
> 
>> sub print_blast_results{
>>    my $report = shift;
>>    while(my $result = $report->next_result()){
> 
> [snip]
> 
> You didn't give us your sort_results subroutine, but is it as simple as 
> they both use $report->next_result (and/or $result->next_hit), but you 
> don't reset the internal counter back to the start, so the second 
> subroutine tries to get the next_result and finds the first subroutine 
> has already looked at the last result and so next_result returns false?
> 
>  From a quick look it wasn't obvious how to reset the counter. Hopefully 
> this can be done and someone else knows how.
>