[Bioperl-l] results problem with StandAloneBlast

Chris Fields cjfields at uiuc.edu
Sat Jun 3 15:13:22 EDT 2006


Nice!  Didn't know I could do that.  Maybe we should add some of this  
to the HOWTO (or is it already in there?).

Chris

On Jun 3, 2006, at 10:29 AM, Jason Stajich wrote:

> you can get all the Hits or hsps with the following method:
> my @hits = $result->hits;
> my @hsps = $hit->hsps;
>
>
> You can also reset the counter since these implementations are in-
> memory and already parsed (and not a stream processor per se).
> next_XX just iterates through the list stored in the parent object.
>
> $result->rewind;
>
>    and
>
> $hit->rewind;
>
>
> For example, the rewind needs to be called if you want to use a
> ResultWriter object and filter some of the values for the final
> writing after first inspecting them.
>
> -jason
>
>
> On May 30, 2006, at 12:57 PM, Genevieve DeClerck wrote:
>
>> 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.
>>>
>>
>> _______________________________________________
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>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> --
> Jason Stajich
> Duke University
> http://www.duke.edu/~jes12
>
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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