[Bioc-sig-seq] PairwiseAlignedXStringSet to PairwiseAlignedFixedSubject

[Patrick Aboyoun]

Stefan,
In this situation, rather than creating a new class, e.g. 
BStringSetList, I would rather encourage use of the pattern() and 
subject() extraction function, which return (Quality)AlignedXStringSet 
objects, that can then in turn be passed to the aligned method. You will 
get the values you are looking for, but without the need for additional 
classes. Here is an example:

 > library(Biostrings)
 > aln <- pairwiseAlignment(c("able", "baker"), c("charlie", "dog"))
 > aln[1]
Global PairwiseAlignedXStringSet (1 of 1)
pattern: [1] abl-e
subject: [3] arlie
score: -14.36196
 > aln[2]
Global PairwiseAlignedXStringSet (1 of 1)
pattern: [1] bak
subject: [1] dog
score: -36.92151
 > aligned(pattern(aln))
   A BStringSet instance of length 2
     width seq
[1]     5 abl-e
[2]     3 bak
 > aligned(subject(aln))
   A BStringSet instance of length 2
     width seq
[1]     5 arlie
[2]     3 dog


Patrick


On 8/4/10 9:02 AM, Stefan Bentink wrote:
> Patrick and Kasper,
> Thanks for your immediate response. I see the problem. However, 
> aligned(pwAligned) would be enough
> at least for my application. And it should be possible to implement 
> (returning a BStringSetList?) .
> Thanks,
> Stefan
>
>
>
> Patrick Aboyoun wrote:
>> Stefan,
>> While it would be possible to convert a PairwiseAlignedFixedSubject 
>> (all patterns aligned to one subject) object to 
>> PairwiseAlignedXStringSet (patterns and subjects are paired during 
>> alignments) object, going the direction you are looking for would not 
>> be possible. As Kasper mentioned, what can be done instead is adding 
>> more methods for PairwiseAlignedXStringSet objects. If you list them 
>> out, I'll see what can be done since not all operations, e.g. 
>> consensusMatrix, that are applicable to the former class make much 
>> sense with the later one.
>>
>>
>> Cheers,
>> Patrick
>>
>>
>>
>> On 8/4/10 8:12 AM, Kasper Daniel Hansen wrote:
>>> Most likely these functions just needs to be implemented for both
>>> classes, at least that is what I suspect Patrick will answer.
>>>
>>> So far you have listed
>>>    as.character
>>>    bi-directional conversion between the two classes (whihc may or may
>>> not make sense)
>>>
>>> You seem to be alluding to other methods not being implemented.  If
>>> that is the case, you should just list all of them, that will make it
>>> much easier to fix.
>>>
>>> Kasper
>>>
>>> On Wed, Aug 4, 2010 at 11:04 AM, Stefan Bentink
>>> <bentink at jimmy.harvard.edu>  wrote:
>>>> Dear List Members,
>>>> I'm using the function pairwiseAlignment from the Biostrings package.
>>>> Depending on the
>>>> input, the function returns either a PairwiseAlignedFixedSubject 
>>>> (if you
>>>> align a single pattern
>>>> with a single subject) or a PairwiseAlignedXStringSet (if you align 
>>>> multiple
>>>> patterns with one
>>>> or more subjects). There are some accessors which work on
>>>> PairwiseAlignedFixedSubject
>>>> objects but not on PairwiseAlignedXStringSet objects. To use those 
>>>> accessors
>>>> on a single
>>>> element from a PairwiseAlignedXStringSet, one would have to make it a
>>>> PairwiseAlignedFixedSubject.
>>>> Is there any way to do that? Subsetting doesn't work since it still 
>>>> returns
>>>> a PairwiseAlignedXStringSet.
>>>> Thanks,
>>>> Stefan
>>>>
>>>>
>>>> Code example:
>>>> library(Biostrings)
>>>> pattern1<- c("ACGT")
>>>> pattern2<- c("CAGT")
>>>> subject1<- c("CAACGTGGAT")
>>>> subject2<- c("GAACAGTAAT")
>>>>
>>>> mat<- nucleotideSubstitutionMatrix(match = 1, mismatch = 0, baseOnly =
>>>> FALSE)
>>>> pwAligned<-
>>>> pairwiseAlignment(c(pattern1,pattern2),c(subject1,subject2),substitutionMatrix=mat,type="local") 
>>>>
>>>>
>>>> ##This throws an error message:
>>>> ##as.character(pwAligned[1])
>>>> ##how to make pwAligned[1] a PairwiseAlignedFixedSubject?
>>>>
>>>>
>>>>> sessionInfo()
>>>> R version 2.12.0 Under development (unstable) (2010-04-07 r51635)
>>>> x86_64-unknown-linux-gnu
>>>>
>>>> locale:
>>>> [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>>>> [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>>>> [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>>>> [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>>>> [9] LC_ADDRESS=C               LC_TELEPHONE=C
>>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>>>
>>>> attached base packages:
>>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>>
>>>> other attached packages:
>>>> [1] BSgenome.Hsapiens.UCSC.hg19_1.3.16 BSgenome_1.17.6
>>>> [3] Biostrings_2.17.26                 GenomicRanges_1.1.19
>>>> [5] IRanges_1.7.15
>>>>
>>>> loaded via a namespace (and not attached):
>>>> [1] Biobase_2.9.0 tools_2.12.0
>>>>
>>>>
>>>>
>>>>
>>>> -- 
>>>> Stefan Bentink
>>>> Research Fellow
>>>> Department of Biostatistics and
>>>> Computational Biology
>>>> Dana-Farber Cancer Institute
>>>> 44 Binney St.
>>>> Boston, MA 02115
>>>>
>>>> Tel: (+1) 617-582-7604
>>>> Fax: (+1) 617-582-7760
>>>>
>>>> bentink at jimmy.harvard.edu
>>>> http://www.hsph.harvard.edu/research/stefan-bentink/
>>>>
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>>>>
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>>
>
>