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pm16057
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@pm16057-12148
Last seen 7.3 years ago
Hi all,
I have been experiencing some difficulties with the "getSeq" function from BSgenome. I have used this functions many times in the past and it has always worked fine but now I keep getting the same error. I have a feeling that something has changed in the package but even after going through gitHub and having a look at the source code I can't seem to locate the error.
Thank you in advance for your help
DNASequence<-getSeq(BSgenome.Dmelanogaster.UCSC.dm6) Error in base::which(x, arr.ind, useNames, ...) : argument to 'which' is not logical
After traceback()
11: base::which(x, arr.ind, useNames, ...)
10: which(strand == "-")
9: which(strand == "-")
8: loadSubseqsFromStrandedSequence(x@single_sequences, seqname,
ranges(gr), strand(gr), is_circular)
7: FUN(X[[i]], ...)
6: lapply(seq_len(length(grl)), function(i) {
gr <- grl[[i]]
if (length(gr) == 0L)
return(DNAStringSet())
seqlevel <- grl_seqlevels[i]
is_circular <- isCircular(x)[[seqlevel]]
idx <- match(seqlevel, x@user_seqnames)
if (is.na(idx))
stop("invalid sequence name: ", seqlevel)
seqname <- names(x@user_seqnames)[[idx]]
if (is.null(snplocs(x, seqname))) {
subject <- try(get(seqname, envir = x@.seqs_cache, inherits = FALSE),
silent = TRUE)
if (is(subject, "try-error")) {
ans <- loadSubseqsFromStrandedSequence(x@single_sequences,
seqname, ranges(gr), strand(gr), is_circular)
return(ans)
}
.linkToCachedObject(subject) <- .newLinkToCachedObject(seqname,
x@.seqs_cache, x@.link_counts)
}
else {
subject <- x[[seqlevel]]
}
masks(subject) <- NULL
loadSubseqsFromStrandedSequence(subject, seqlevel, ranges(gr),
strand(gr), is_circular)
})
5: lapply(seq_len(length(grl)), function(i) {
gr <- grl[[i]]
if (length(gr) == 0L)
return(DNAStringSet())
seqlevel <- grl_seqlevels[i]
is_circular <- isCircular(x)[[seqlevel]]
idx <- match(seqlevel, x@user_seqnames)
if (is.na(idx))
stop("invalid sequence name: ", seqlevel)
seqname <- names(x@user_seqnames)[[idx]]
if (is.null(snplocs(x, seqname))) {
subject <- try(get(seqname, envir = x@.seqs_cache, inherits = FALSE),
silent = TRUE)
if (is(subject, "try-error")) {
ans <- loadSubseqsFromStrandedSequence(x@single_sequences,
seqname, ranges(gr), strand(gr), is_circular)
return(ans)
}
.linkToCachedObject(subject) <- .newLinkToCachedObject(seqname,
x@.seqs_cache, x@.link_counts)
}
else {
subject <- x[[seqlevel]]
}
masks(subject) <- NULL
loadSubseqsFromStrandedSequence(subject, seqlevel, ranges(gr),
strand(gr), is_circular)
})
4: .extractFromBSgenomeSingleSequences(x, sseq_args$names, sseq_args$start,
sseq_args$end, sseq_args$width, sseq_args$strand)
3: .local(x, ...)
2: getSeq(BSgenome.Dmelanogaster.UCSC.dm6)
1: getSeq(BSgenome.Dmelanogaster.UCSC.dm6)
And SessionInfo()
sessionInfo() R version 3.3.2 (2016-10-31) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 14.04.5 LTS locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets [8] methods base other attached packages: [1] BSgenome.Dmelanogaster.UCSC.dm6_1.4.1 BSgenome_1.42.0 [3] rtracklayer_1.34.1 Biostrings_2.42.1 [5] XVector_0.14.0 GenomicRanges_1.26.2 [7] GenomeInfoDb_1.10.2 IRanges_2.8.1 [9] S4Vectors_0.12.1 BiocGenerics_0.20.0 [11] BiocInstaller_1.24.0 loaded via a namespace (and not attached): [1] lattice_0.20-34 XML_3.98-1.5 [3] Rsamtools_1.26.1 GenomicAlignments_1.10.0 [5] bitops_1.0-6 grid_3.3.2 [7] zlibbioc_1.20.0 Matrix_1.2-7.1 [9] BiocParallel_1.8.1 tools_3.3.2 [11] Biobase_2.34.0 RCurl_1.95-4.8 [13] SummarizedExperiment_1.4.0
You were right! I had to reinstall R. but it did the trick! Thank you for your help