[Biojava-dev] Using DNASequence reverseComplement
LAW Andrew
andy.law at roslin.ed.ac.uk
Tue May 18 09:10:30 UTC 2010
Another philosophical question from the sidelines.
Does a BJ3 object return a *new* object when asked for a reverseComplement/subSequence/whatever (I suspect from what I have read here and heard from Trevor that it does not)?
Should it?
If I have DNA sequence object A and I ask it for the reverseComplement of the last 16 bases (call it sequence B) and then modify sequence A to change the last base (if that is possible?), what would happen to the sequence B? (And what do we think *should* happen to sequence B)?
On 18 May 2010, at 10:00, PATERSON Trevor wrote:
> Hi andy
>
> I know this is all work in progress so I'm not too hung up on everything not working out the box..
>
> What I am doing is stitching together contigs into an assembly, so I have an AssembledDNASequence Object,
> that extends DNASequence but defers its method to an Assembly Object which contains a Map of DNASequences
> with ranges and orientations. This map is created from a single SQL call, and is populated with DNASequence
> Objects that lazy load their actual sequence data from the database when required
>
> The only way I can check that the map is giving my the correct assembly is to print out
> the sequence as string of each component in order,
> ie
> Frag 1, from 1 to 200
> Gap of 150 N
> Frag 2, from 1 to 5000 REVERSED
> Frag 3, from 150 to 6000
> Gap of 2000 N
>
> etc
>
> I think your suggestion actually demonstrates the 'bug' ( or 'feature' ;)
>
> seq.getReverseComplement().getSubSequence(1,4).getSequenceAsString()
> returns the whole reverse complement - not just 1-4: AACCCGGGGTTTTT
> Because the getSequenceAsString is looking at the parent of the view :
>
> Something even more horrible happens if you try to bound that query
> seq.getReverseComplement().getSubSequence(1,4).getSequenceAsString(1,4,Strand.POSITIVE)
> Returns AAAA ( ie this is 1-4 of the parent, not even the reverse complement.)
> And perhaps more interestingly
> seq.getReverseComplement().getSubSequence(1,4).getSequenceAsString(1,4,Strand.NEGATIVE))
> Also returns AAAA (which I just plain can't understand..)
>
> ___________________________________________________________________________________
>
> Anyway - I am probably at a stage where I don't want to do any more development on this at the moment...
> I am reasonably happy that an EnsemblAPI will be able to use the BioJava Sequence objects down the road.
>
> I have made an EnsemblDNASequenceReader that extends and implements ProxySequenceReader
> This is used to create a DataSourceAwareDNASequence and responsible for lazy loading the actual sequence data
> from Ensembl when required
>
> To do this I needed to give the AbstractSequences's (SequenceReader) sequenceStorage property and its getter protected rather
> than private access, because there needs to be exchange of info from one to the other
>
> I will need to implement some sort of chunking and caching for retrieval of larger sequences, and maybe even pass
> all the methods to a buffered reader for large sequences, but I'm not going to worry about this at the moment.
>
> There are plenty of other things for me to protoype in ensembl at the moment!
>
> Cheers Trevor
>
>
>
>
>
>
>
>
>> -----Original Message-----
>> From: Andy Yates [mailto:andyyatz at gmail.com] On Behalf Of Andy Yates
>> Sent: 17 May 2010 17:08
>> To: PATERSON Trevor
>> Cc: biojava-dev at lists.open-bio.org
>> Subject: Re: [Biojava-dev] Using DNASequence reverseComplement
>>
>> Hi Trevor,
>>
>> You've stumbled right into something myself & Scooter are
>> trying to clean-up now. The assumption I had originally made
>> is that all operations on things like getSequenceAsString()
>> would go via the view since that's where the logic is located
>> for both the reversing & the complementing code. That call
>> now delegates onto the backing store and not the view which
>> means you get these very odd results happening.
>>
>> For the moment I think the following code would do what
>> you're expecting:
>>
>> seq.getReverseComplement().getSubSequence(1,4).getSequenceAsString()
>>
>> It's annoying because you're in the reverse coordinate system
>> you've got to reverse the original coordinates so asking for
>> position 11,14 just isn't going to work. The other way of
>> working with this would be to construct the views yourself
>> and pass in a subsequence of the original sequence i.e.
>>
>> new ReversedSequenceView<NucleotideCompound>(new
>> ComplementSequenceView<NucleotideCompound>(seq.getSubSequence(11,14));
>>
>> This is really a problem with the erasure of the Sequence
>> types from DNASequence. If DNASequence returned the same type
>> from its subsequence method then you would just call revComp
>> on that and it would have been fine.
>>
>> The thing to take away from are:
>>
>> * getSequenceAsString(Integer, Integer, Strand) is not well
>> supported atmo
>>
>> * So long as we are sure it should remain it will be
>>
>> * There should be no reason to materialise the Sequence into
>> a String to get a part of the API working. If there is then
>> we've messed up
>>
>> Andy
>>
>> p.s. The strand stuff is confusing; originally it was meant
>> to be +ve & -ve strands but assumed that the Sequence you had
>> was always on the +ve strand. Eventually the meaning will
>> come back but will require the methods to be more aware of
>> the strand DNA is on to make the right call about what you
>> want to do. This all ties in with circular genomes support
>> and locations
>>
>> On 17 May 2010, at 16:24, PATERSON Trevor wrote:
>>
>>> Sorry for raising that behemoth earlier..
>>>
>>> I have a separate problem with the DNASequence API -
>>>
>>> Probably I just don't understand how to use the View objects
>>>
>>>
>>> If I make a DNASequence
>>>
>>> DNASequence seq = new DNASequence("AAAAACCCCGGGTT");
>>>
>>> i.e. length = 14,
>>>
>>> I might reasonably want to get the ReverseComplement of
>> bases 11-14, which should 'be' "AACC"
>>>
>>> But I cannot manage to get this in one easy step....
>>>
>>> seq.toString(): AAAAACCCCGGGTT --> FINE
>>>
>>> seq.getReverseComplement().getSequenceAsString():
>> AACCCGGGGTTTTT -->
>>> FINE
>>>
>>> But when I try to use bounds on this complement - methods
>> refer back
>>> to the original seq's iterator, not the complement
>>>
>>>
>> seq.getReverseComplement().getSequenceAsString(11,14,Strand.PO
>> SITIVE): GGTT
>>> i.e the same as seq.getSequenceAsString(11,14,Strand.POSITIVE)
>>>
>> seq.getReverseComplement().getSequenceAsString(11,14,Strand.NE
>> GATIVE): TTGG
>>> i.e the same as seq.getSequenceAsString(11,14,Strand.NEGATIVE)
>>>
>>> Is this the desired behaviour? How would I get the desired
>> reverseComplement fragment?
>>>
>>> The only obvious way that I can see is
>>>
>>> DNASequence subseq = new
>> DNASequence(seq.getSequenceAsString(11, 14, Strand.POSITIVE));
>>> System.out.println(""+
>>> subseq.getReverseComplement().getSequenceAsString());
>>>
>>>
>> ______________________________________________________________________
>>> _______________________
>>>
>>> On a related point I was mightily confused by the
>>> Strand.POSITIVE/Strand.NEGATIVE enumeration
>>>
>>> I was naively interpreting them to refer to the strand of the DNA:
>>> Whereas they infact refer to the directionality of the Iterator *on
>>> the same Strand*
>>>
>>> A better name might be Direction:FORWARDS/Direction.BACKWARDS?
>>> Positive and negative strand has loaded biological meaning
>> for newbies
>>> like me ( sense versus antisense ) So I made the assumption that a
>>> Strand.NEGATIVE call would itself reverseComplement
>>> --
>>> The University of Edinburgh is a charitable body, registered in
>>> Scotland, with registration number SC005336.
>>>
>>>
>>> _______________________________________________
>>> biojava-dev mailing list
>>> biojava-dev at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>
>> --
>> Andrew Yates Ensembl Genomes Engineer
>> EMBL-EBI Tel: +44-(0)1223-492538
>> Wellcome Trust Genome Campus Fax: +44-(0)1223-494468
>> Cambridge CB10 1SD, UK http://www.ensemblgenomes.org/
>>
>>
>>
>>
>>
> --
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
>
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Later,
Andy
--------
Yada, yada, yada...
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