GenomicFeatures::getPromoterSeq error when selecting all promoters sequences (in mice)
1
0
Entering edit mode
@branislav-misovic-4248
Last seen 2.5 years ago
Netherlands/Amsterdam

hi ,

  When running the search for all promoters sequences  in mice , with  1000 bp  up /downstream, parameter the getPromoterSeq  works fine,  but increasing the up/downstream parameter to say 5000  or 2000 it errors  (log bellow):

Any advice appreciated .
Branko
-------------------------------------------

library(GenomicFeatures)
library(BSgenome.Mmusculus.UCSC.mm10)
library(TxDb.Mmusculus.UCSC.mm10.knownGene)  

chr.loc = transcriptsBy (TxDb.Mmusculus.UCSC.mm10.knownGene, by = "gene")
system.time ( prom.all <- getPromoterSeq(chr.loc, Mmusculus, upstream=2000, downstream=1000))

Error in loadFUN(x, seqname, ranges) :
  trying to load regions beyond the boundaries of non-circular sequence "chr4_JH584294_random"

In addition: Warning messages:
1: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
  GRanges object contains 1 out-of-bound range located on sequence
  chr4_JH584294_random. Note that only ranges located on a non-circular

........
--------------------

14: stop("trying to load regions beyond the boundaries ", "of non-circular sequence \"",
        seqname, "\"")
13: loadFUN(x, seqname, ranges)
12: loadFUN(x, seqname, ranges)
11: loadSubseqsFromStrandedSequence(x@single_sequences, seqname,
        ranges(gr), strand(gr), is_circular)
10: FUN(1:35[[27L]], ...)
9: 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)
   })
8: 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)
   })
7: .extractFromBSgenomeSingleSequences(x, sseq_args$names, sseq_args$start,
       sseq_args$end, sseq_args$width, sseq_args$strand)
6: .local(x, ...)
5: getSeq(subject, promoter.granges)
4: getSeq(subject, promoter.granges)
3: getPromoterSeq(chr.loc, Mmusculus, upstream = 2000, downstream = 1000)
2: getPromoterSeq(chr.loc, Mmusculus, upstream = 2000, downstream = 1000)
1: system.time(prom.all <- getPromoterSeq(chr.loc, Mmusculus, upstream = 2000,
       downstream = 1000))


---------------------------------------------

> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-pc-linux-gnu (64-bit)

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=en_US.UTF-8    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] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] TxDb.Mmusculus.UCSC.mm10.knownGene_3.0.0
 [2] BSgenome.Mmusculus.UCSC.mm10_1.4.0
 [3] BSgenome_1.34.0
 [4] rtracklayer_1.26.2
 [5] Biostrings_2.34.0
 [6] XVector_0.6.0
 [7] org.Mm.eg.db_3.0.0
 [8] RSQLite_1.0.0
 [9] DBI_0.3.1
[10] GenomicFeatures_1.18.2
[11] AnnotationDbi_1.28.1
[12] Biobase_2.26.0
[13] GenomicRanges_1.18.1
[14] GenomeInfoDb_1.2.3
[15] IRanges_2.0.0
[16] S4Vectors_0.4.0
[17] BiocGenerics_0.12.1
[18] BiocInstaller_1.16.1

loaded via a namespace (and not attached):
 [1] base64enc_0.1-2         BatchJobs_1.5           BBmisc_1.8
 [4] BiocParallel_1.0.0      biomaRt_2.22.0          bitops_1.0-6
 [7] brew_1.0-6              checkmate_1.5.0         codetools_0.2-9
[10] digest_0.6.4            fail_1.2                foreach_1.4.2
[13] GenomicAlignments_1.2.1 iterators_1.0.7         RCurl_1.95-4.3
[16] Rsamtools_1.18.2        sendmailR_1.2-1         stringr_0.6.2
[19] tools_3.1.1             XML_3.98-1.1            zlibbioc_1.12.0

 

GenomicFeatures getPromoterSeq • 2.0k views
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1
Entering edit mode
@james-w-macdonald-5106
Last seen 1 day ago
United States

It depends on if you care about all the unplaced haplotypes. If not, just nuke them and go forward.

> trs <- transcriptsBy(TxDb.Mmusculus.UCSC.mm10.knownGene, by = "gene")
> trs <- keepStandardChromosomes(trs)

> prom <- getPromoterSeq(trs, Mmusculus, upstream = 2e3, downstream=1e3)

> prom
DNAStringSetList of length 23696
[["100009600"]] CTTCTTCTTTTTCGAGACAGGGTTTCTCTGTGTAGCCCTGGCTATCAACTCAGAAATCCGC...
[["100009609"]] CACCTCACACCTGTCAGAATGGCTAGGATCAAAAATTCAGGTGACAGCAGATGCTGGTGAG...
[["100009614"]] TGGGTGTCTCATTAGCTCTTTGTATAGCTTCTGAGAGTCATAAAGCCTATATGTCAAAACT...
[["100009664"]] CACCTACGGGACTAAATAAAGAGTCAGCACTTTTTGGCAAAAGCAGCCTAAGTCCCTGTTT...
[["100012"]] GTTGTCTTACTAAAGCAAACACTAGGAAGATTGTTTTCCTGAGGCAGGCCAAGGTGGAAAAAGT...
[["100017"]] TGCCTGCCCCTCTTTGACTTATTGATGAGGCCTGCTTCTGGGGAGCAAGATAAGGATGTGGACA...
[["100019"]] AGAAAGTAAAATTAAAGAATGAGTAAGCTGAAAAATCAGGTCAAGAAACTCCCAAAAGGAACCC...
[["100033459"]] AATTTCTGTATCCATTCTTCTGTCATGGGACATCTGGGTTGTTTCCAGCTTTGGGCTATCA...
[["100034251"]] GTCTGAGTGAGGGACACTATAAGAAGTGCACATCCAATCAGCAATGAGCTAATGAGCAGAG...
[["100034361"]] TGCAGGATCTAAATCAGCACTTACACTGGATCCTGTAATATTGAGCCCAGTCTACTCCTCC...
...
<23686 more elements>

 

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0
Entering edit mode

thank you ,  also for the lesson about unplaced ones ...

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