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

[Chris Fields]

That sounds like a bug.  Does filtering at the hit level work around this?

sub hit_filter {
   my $hit = shift;
   # filter hsps here
   my @passing_hsps = grep { hsp_filter($_) } $hit->hsps;
   @passing_hsps;
}

sub hsp_filter {
   # original filter
}

chris

On May 31, 2010, at 4:19 AM, Remi wrote:

> Hi,
> 
> Everything is working well but there is still one point that giving me some trouble.
> When I filter the hsps and all the hsps of a given hit are removed, the description line of the hit is still present in the HTML file.
> Is there a way to get rid of this description line ?
> Is the only solution to inherit from Bio::SearchIO::Writer::HTMLWriter and overriding the "to_string" method ?
> 
> Thanks,
> 
> Rémi
> 
> 
> Chris Fields wrote:
>> 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
>>>>>> 
>>>>>> 
>>>>>>  
>>>>>>       
>>>>>> 
>>>>>>           
>>>>>> 
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> 
>>>>> 
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>> 
>>>>> 
>>>>>     
>>>>> 
>>>>>         
>>>>> 
>>>>   
>>>> 
>>>>       
>>>> 
>> 
>>   
>> 
>