[Bioperl-l] Clear range from Bio::Seq::Quality?

Heikki Lehvaslaiho heikki.lehvaslaiho at gmail.com
Mon Apr 27 11:44:40 EDT 2009


Dan,

Have a look at Bio/Seq/Quality.pm and t/Seq/Quality.t in bioperl-live.

Test and extend,

    -Heikki

2009/4/27 Heikki Lehvaslaiho <heikki.lehvaslaiho at gmail.com>:
> Dan,
>
> I'll take your code and put it into bioperl-live rewritten the way I
> suggested and add few tests.
>
> That should get you started,
>
>   -Heikki
>
> 2009/4/27 Dan Bolser <dan.bolser at gmail.com>:
>> Hi Heikki,
>>
>> Thanks very much for the advice on how to better implement the clear
>> range method within the Bio::Seq::Quality object. I can understand the
>> logic of what you have written, and it all sounds reasonable. The only
>> problem is that I am very inexperienced with working on object
>> oriented Perl (my 'one man' projects to date have never really
>> required me to think beyond scripts, and its been years since I
>> actually tried to code objects in Perl).
>>
>> To be specific, when you say, "Lets add a method that sets the
>> threshold and stores it internally as $self->_threshold", ignoring any
>> other functionality, what would that method look like? in particular,
>> how would $self->_threshold be implemented?
>>
>> I think once I see that detail, I can go ahead and try to code what
>> you suggested.
>>
>>
>> Similarly (Chris), where would I put the tests / how would they be implemented?
>>
>>
>> Thanks again for the feedback.
>>
>> All the best,
>> Dan.
>>
>>
>>
>> 2009/4/27 Heikki Lehvaslaiho <heikki.lehvaslaiho at gmail.com>:
>>> Dan,
>>>
>>> It looks like your method does two different things:
>>>
>>> 1. Returns the longest subsequence above the threshold
>>> 2. Analyses the the sequence for the number of ranges the current
>>> threshold creates.
>>>
>>> Why not separate these functions?
>>>
>>> Lets add a method that sets the threshold and stores it internally as
>>> $self->_threshold. Setting it to a new values should trigger emptying
>>> all the caches (see below.)
>>>
>>> Lets have two more public methods:
>>>
>>> 1. get_clean_range() - optional argument 'threshold'
>>>
>>> It returns the longest clean subseq.
>>>
>>> 2. count_clean_ranges() -again optional argument 'threshold'
>>>
>>> This returns the number of ranges detected.
>>>
>>> Both methods call first the public method threshold if the argument
>>> has been given and then an internal method  _find_clean_ranges(). That
>>> method calculates all the ranges and stores them internally  (as
>>> $self->_clean_ranges-> [...]). The number of ranges is also stored
>>> (e.g. $self->_number_of ranges).These internal values form  the cache
>>> that needs to be emptied whenever any of the critical values of the
>>> object changes: threshold, quality or seq. Create an internal method
>>> $self->_clear_cache, that does that.
>>>
>>> Now the quality new object does not get created until you call
>>> get_clean_range() which accesses the cached values (or creates them if
>>> they are not there).
>>>
>>> This design allows you to have no extra penalty for adding more
>>> methods that act on cached values. For example, it might be sensible
>>> thing to do  at some point to look at all the ranges that are longer
>>> than some length. Then you could write in your program:
>>>
>>>
>>> $qual->threshold(10);
>>> if ($qual->count_clean_ranges = 1) {
>>>  my $newqual = $qual->get_clean_range()
>>>  # do your analysis
>>> } elsif ($qual->count_clean_ranges = 0) {
>>>   # do some reporting and logging
>>> } else {  # more than one ranges
>>>   my @quals = $qual->get_all_clean_ranges($min_lenght);
>>>   # do some more work and possibly select the best one(s)
>>> }
>>>
>>>
>>>
>>> Yours,
>>>
>>>   -Heikki
>>>
>>> 2009/4/24 Chris Fields <cjfields at illinois.edu>:
>>>> You could submit this as a diff against Bio::Seq::Quality to bugzilla.  If
>>>> possible, tests don't hurt either!
>>>>
>>>> chris
>>>>
>>>> On Apr 24, 2009, at 11:20 AM, Dan Bolser wrote:
>>>>
>>>>> Its a bit rough and ready, but it does what I need...
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> =head2 get_clear_range
>>>>>
>>>>> Title    : get_clear_range
>>>>>
>>>>> Title    : subqual
>>>>> Usage    : $subobj = $obj->get_clear_range();
>>>>>           $subobj = $obj->get_clear_range(20);
>>>>> Function : Get the clear range using the given quality score as a
>>>>>           cutoff or a default value of 13.
>>>>>
>>>>> Returns  : a new Bio::Seq::Quality object
>>>>> Args     : a minimum quality value, optional, devault = 13
>>>>>
>>>>> =cut
>>>>>
>>>>> sub get_clear_range
>>>>> {
>>>>>   my $self = shift;
>>>>>   my $qual = $self->qual;
>>>>>   my $minQual = shift || 13;
>>>>>
>>>>>   my (@ranges, $rangeFlag);
>>>>>
>>>>>   for(my $i=0; $i<@$qual; $i++){
>>>>>        ## Are we currently within a clear range or not?
>>>>>        if(defined($rangeFlag)){
>>>>>            ## Did we just leave the clear range?
>>>>>            if($qual->[$i]<$minQual){
>>>>>                ## Log the range
>>>>>                push @ranges, [$rangeFlag, $i-1, $i-$rangeFlag];
>>>>>                ## and reset the range flag.
>>>>>                $rangeFlag = undef;
>>>>>            }
>>>>>            ## else nothing changes
>>>>>        }
>>>>>        else{
>>>>>            ## Did we just enter a clear range?
>>>>>            if($qual->[$i]>=$minQual){
>>>>>                ## Better set the range flag!
>>>>>                $rangeFlag = $i;
>>>>>            }
>>>>>            ## else nothing changes
>>>>>        }
>>>>>   }
>>>>>   ## Did we exit the last clear range?
>>>>>   if(defined($rangeFlag)){
>>>>>        my $i = scalar(@$qual);
>>>>>        ## Log the range
>>>>>        push @ranges, [$rangeFlag, $i-1, $i-$rangeFlag];
>>>>>   }
>>>>>
>>>>>   unless(@ranges){
>>>>>        die "There is no clear range... I don't know what to do here!\n";
>>>>>   }
>>>>>
>>>>>   print "there are ", scalar(@ranges), " clear ranges\n";
>>>>>
>>>>>   my $sum; map {$sum += $_->[2]} @ranges;
>>>>>
>>>>>   print "of ", scalar(@$qual), " bases, there are $sum with ".
>>>>>        "quality scores above the given threshold\n";
>>>>>
>>>>>   for (sort {$b->[2] <=> $a->[2]} @ranges){
>>>>>        if($_->[2]/$sum < 0.5){
>>>>>            warn "not so much a clear range as a clear chunk...\n";
>>>>>        }
>>>>>        print $_->[2], "\t", $_->[2]/$sum, "\n";
>>>>>
>>>>>        return Bio::Seq::QualityDB->new( -seq => $self->subseq(  $_->[0]+1,
>>>>> $_->[1]+1),
>>>>>                                         -qual => $self->subqual($_->[0]+1,
>>>>> $_->[1]+1)
>>>>>                                         );
>>>>>   }
>>>>> }
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> Note, for testing I made a package called Bio/Seq/QualityDB.pm (which
>>>>> is a copy of Bio/Seq/Quality.pm that just has the above method added).
>>>>> That is why the 'new Bio::Seq::Quality object' is actually a
>>>>> Bio::Seq::QualityDB object, but other than that it should slot right
>>>>> in (apart from all the debugging output that I spit out).
>>>>>
>>>>>
>>>>> Cheers,
>>>>> Dan.
>>>>>
>>>>>
>>>>> 2009/4/24 Dan Bolser <dan.bolser at gmail.com>:
>>>>>>
>>>>>> Hi all,
>>>>>>
>>>>>> I couldn't find out how to get the 'clear range' from a
>>>>>> Bio::Seq::Quality object... Am I looking in the wrong place, or should
>>>>>> this method be a part of the Bio::Seq::Quality class?
>>>>>>
>>>>>> In the latter case I'm on my way to an implementation, but I am not
>>>>>> good at navigating the bioperl docs, so I thought I should ask before
>>>>>> I take the time to finish that off.
>>>>>>
>>>>>>
>>>>>> Cheers,
>>>>>> Dan.
>>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
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>>>>
>>>
>>>
>>>
>>> --
>>>    -Heikki
>>> Heikki Lehvaslaiho - skype:heikki_lehvaslaiho
>>> cell: +27 (0)714328090
>>> Sent from Claremont, WC, South Africa
>>>
>>
>
>
>
> --
>    -Heikki
> Heikki Lehvaslaiho - skype:heikki_lehvaslaiho
> cell: +27 (0)714328090
> Sent from Claremont, WC, South Africa
>



-- 
    -Heikki
Heikki Lehvaslaiho - skype:heikki_lehvaslaiho
cell: +27 (0)714328090
Sent from Claremont, WC, South Africa



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