[Bioperl-l] Cloning Bio::Search::Result::GenericResult

[Chris Fields]

Let us know how it goes, and if you run into any bugs.

chris

On May 28, 2010, at 9:31 AM, Remi wrote:

> Thank you very much !!!!
> I'm gonna try it right away
> 
> Chris Fields wrote:
>> Remi,
>> 
>> Using the constructor that way is not supported.  But it's completely unnecessary.  
>> 
>> Are you using Bio::SearchIO::Writer::HTMLWriter?  It filters results/hits/HSPs as it writes the HTML, no need to clone.  That in combination with GenericResult::rewind() should work.  You can use that module, or inherit and override whatever methods are necessary.  Or just use it as a reference on how to do what you need.  
>> 
>> Something like the following should work (of course completely untested :)
>> 
>> my $result = $in->next_result;
>> 
>> # filter on HSP
>> write_html('result1.html', $result, { 'HSP' => \&hsp_filter });
>> 
>> # rewind the result to go back to the beginning
>> $result->rewind;
>> 
>> # open a new filehandle here for second report output
>> # filter on hit and HSP
>> write_html('result2.html', $result, { 'HIT' => \&hit_filter,
>>                            'HSP' => \&hsp_filter });
>> 
>> # rewind the result to go back to the beginning
>> $result->rewind;
>> 
>> # and so on....
>> 
>> sub write_html {
>>     my ($file, $result, $filters) =  @_;
>>     # note that $filter is a hash ref above
>>     my $writer = Bio::SearchIO::Writer::HTMLResultWriter->new
>>                      (-filters => $filters );
>> 
>>     my $out = Bio::SearchIO->new(-writer => $writer, -file => $file); 
>>     $out->write_result($result);
>> }
>> 
>> sub hsp_filter { 
>>     my $hsp = shift;
>>     return 1 if $hsp->length('total') > 100;
>> }
>> 
>> sub hit_filter { 
>>     my $hit = shift;
>>     return 1 if $hit->significance < 1e-5;
>> }
>> 
>> chris
>> 
>> 
>> On May 28, 2010, at 7:17 AM, Remi wrote:
>> 
>>   
>> 
>>> You're right, it's not working there is some missing fields ...
>>> 
>>> Actually, I'm writing a script that filter Result Object based on some criteria and I want the script to be kind of interactive like :
>>> 
>>> -Display Result object as HTML
>>> -Ask for filter criteria
>>> -Filter Result object
>>> -Display filtered Result object as HTML.
>>> ... etc
>>> 
>>> And I would like to make a copy of the Result object before each filtering step in order to be able to redo it.
>>> 
>>> I'll have a look to the modules you've mentioned, thanks.
>>> 
>>> 
>>> 
>>> 
>>> Dave Messina wrote:
>>>     
>>> 
>>>> Hi Rémi,
>>>> 
>>>> As far as I know, cloning objects is not natively supported in BioPerl (or Perl itself, for that matter).
>>>> 
>>>> So I don't think the code you showed will work.
>>>> 
>>>> However, there are modules such as Clone::More and Clone::Fast that can do it.
>>>> 
>>>> 
>>>> http://search.cpan.org/~wazzuteke/Clone-More-0.90.2/lib/Clone/More.pm
>>>> http://search.cpan.org/~wazzuteke/Clone-Fast-0.93/lib/Clone/Fast.pm
>>>> 
>>>> 
>>>> 
>>>> Out of curiosity, what are you trying to do with the cloned objects? Someone might be able to suggest another way to accomplish the same goal.
>>>> 
>>>> Dave
>>>> 
>>>> 
>>>>  
>>>>       
>>>> 
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>>> 
>>>     
>>> 
>> 
>>   
>> 
>