This is a sensible request, as it would be consistent with the behavior for
RangesList and RangedData. Anyone opposed to this change?

On Tue, Nov 30, 2010 at 6:43 AM, Anna Terry <anna.terry@csc.mrc.ac.uk>wrote:

> Hi,
>
> Would it be possible for the BSgenome function getSeq to return the +
> strand by default when given a GRanges object where the strand is "*" rather
> than throw an error?  The strand is not known for ChIP-seq regions and so it
> is sensible to have the strand as "*" when storing them in a GRanges object.
>
> Anna
>
> > problem.gr
> GRanges with 1 range and 6 elementMetadata values
>    seqnames                 ranges strand |     score     count    unique
> <Rle> <IRanges> <Rle> | <numeric> <integer> <integer>
> [1]     chr5 [125821746, 125821945]      * |  97.02651       124       116
>    ref.count    height       max
> <integer> <numeric> <numeric>
> [1]        10  29.03108 125821846
>
> seqlengths
>         chr1         chr2         chr3 ...  chrY_random chrUn_random
>    197195432    181748087    159599783 ...     58682461      5900358
>
> > problem.seq <- getSeq(Mmusculus, problem.gr)
> Error in .extractSeqsFromDNAString(subject, ranges(grg), strand(grg)) :
>  'strand' elements must be "+" or "-"
> Calls: getSeq ... lapply -> lapply -> FUN -> .extractSeqsFromDNAString
>
> > problem.seq <- getSeq(Mmusculus, problem.gr, strand="+")
> Error in .extractSeqsFromDNAString(subject, ranges(grg), strand(grg)) :
>  'strand' elements must be "+" or "-"
> Calls: getSeq ... lapply -> lapply -> FUN -> .extractSeqsFromDNAString
>
> > problem.seq <- getSeq(Mmusculus, seqnames(problem.gr), start=start(
> problem.gr), end=end(problem.gr))
> # works
>
>
> > sessionInfo()
> R version 2.11.1 (2010-05-31)
> x86_64-redhat-linux-gnu
>
> locale:
>  [1] LC_CTYPE=en_GB          LC_NUMERIC=C            LC_TIME=en_GB
>  [4] LC_COLLATE=en_GB        LC_MONETARY=en_GB       LC_MESSAGES=en_GB
>  [7] LC_PAPER=en_GB          LC_NAME=en_GB           LC_ADDRESS=en_GB
> [10] LC_TELEPHONE=en_GB      LC_MEASUREMENT=en_GB
>  LC_IDENTIFICATION=en_GB
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] XML_3.2-0                          BSgenome.Mmusculus.UCSC.mm9_1.3.16
> [3] BSgenome_1.16.5                    GenomicRanges_1.0.9
> [5] Biostrings_2.16.9                  IRanges_1.6.17
> [7] rkward_0.5.3
>
> loaded via a namespace (and not attached):
> [1] Biobase_2.8.0 tools_2.11.1
>
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>

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