Merge branch 'dev'

BIMSBbioinfo · Dec 4, 2018 · 15ca013 · 15ca013
2 parents eb5fc37 + f745735
commit 15ca013
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diff --git a/.lintr b/.lintr
@@ -1,5 +1,3 @@
-# Note: There is are two copies of this file (.lintr & inst/.lint) that need to
-# be kept in sync (see https://github.com/jimhester/covr/issues/253)
 # see https://github.com/jimhester/lintr#project-configuration
 linters: with_defaults(
     camel_case_linter = NULL, # 133

diff --git a/.travis.yml b/.travis.yml
@@ -13,10 +13,14 @@ r_github_packages:
 
 # See https://docs.travis-ci.com/user/languages/r/#R-Versions
 r:
-#  - oldrel
+  - oldrel
   - release
   - devel
 
+# See https://github.com/travis-ci/travis-ci/issues/7654#issuecomment-297051230
+# TODO: check for 'latest', 'previous', etc. mappings
+dist: trusty
+
 sudo: required
 bioc_required: true
 

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,3 +1,16 @@
+ciRcus 0.1.6
+------------
+NEW FEATURES
+
+* new bedTracks()/writeBedTracks() functions generating BED6-style
+  GRangesList/writing BED files for circRNA browser tracks
+* added D. melanogaster (dm6) and R. norvegicus (rn6) support
+
+IMPROVEMENTS AND BUG FIXES
+
+* using "coarse" pruning.mode in keepStandardChromosomes when building annotation
+* introduced a number of bugfixes (and probably new bugs)
+
 ciRcus 0.1.5
 ------------
 NEW FEATURES

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -21,20 +21,23 @@ Imports:
     AnnotationDbi,
     AnnotationHub,
     biomaRt,
+    BiocGenerics,
     data.table,
     DBI,
+    GenomeInfoDb,
     GenomicFeatures,
     GenomicRanges,
     ggplot2,
     hash,
     IRanges,
     RColorBrewer,
     RMySQL,
+    rtracklayer,
     S4Vectors,
     stringr,
     SummarizedExperiment
 Suggests:
     testthat,
     knitr,
     lintr
-RoxygenNote: 6.0.1
+RoxygenNote: 6.1.0
diff --git a/NAMESPACE b/NAMESPACE
@@ -8,6 +8,7 @@ export(annotateCircs)
 export(annotateFlanks)
 export(annotateHostGenes)
 export(annotateJunctions)
+export(bedTracks)
 export(circLinRatio)
 export(getStudiesList)
 export(gtf2sqlite)
@@ -18,6 +19,7 @@ export(resTable)
 export(summarizeCircs)
 export(testCoordinateIndexing)
 export(uniqReadsQC)
+export(writeBedTracks)
 import(AnnotationHub)
 import(DBI)
 import(RMySQL)
@@ -28,7 +30,12 @@ import(methods)
 import(stringr)
 importFrom(AnnotationDbi,loadDb)
 importFrom(AnnotationDbi,saveDb)
+importFrom(BiocGenerics,sort)
+importFrom(GenomeInfoDb,"seqlevels<-")
+importFrom(GenomeInfoDb,"seqlevelsStyle<-")
+importFrom(GenomeInfoDb,seqlevelsStyle)
 importFrom(GenomicFeatures,makeTxDbFromGRanges)
+importFrom(GenomicRanges,GRangesList)
 importFrom(GenomicRanges,makeGRangesFromDataFrame)
 importFrom(GenomicRanges,reduce)
 importFrom(GenomicRanges,resize)
@@ -45,3 +52,5 @@ importFrom(data.table,set)
 importFrom(data.table,setnames)
 importFrom(hash,hash)
 importFrom(hash,keys)
+importFrom(rtracklayer,export)
+importFrom(rtracklayer,score)
diff --git a/R/annotate.R b/R/annotate.R
@@ -10,7 +10,8 @@
 #'
 #' @export
 gtf2sqlite <-
-  function(assembly = c("hg19", "hg38", "mm10", "rn5", "dm6", "WBcel235"),
+  function(assembly = c("hg19", "hg38", "mm10", "rn5", "rn6", "dm6",
+                        "WBcel235"),
            db.file) {
 
   ah <- AnnotationHub()
@@ -105,7 +106,7 @@ setMethod("loadAnnotation", signature("character"),
 setGeneric("annotateCircs",
            function(se,
                     annot.list,
-                    assembly = c("hg19", "hg38", "mm10", "rn5", "dm6",
+                    assembly = c("hg19", "hg38", "mm10", "rn5", "rn6", "dm6",
                                  "WBcel235"),
                     fixCoordIndexing = TRUE,
                     ...)
@@ -115,7 +116,7 @@ setGeneric("annotateCircs",
 #' @rdname annotateCircs-methods
 setMethod("annotateCircs", signature("RangedSummarizedExperiment"),
           function(se, annot.list,
-                   assembly = c("hg19", "hg38", "mm10", "rn5", "dm6",
+                   assembly = c("hg19", "hg38", "mm10", "rn5", "rn6", "dm6",
                                 "WBcel235"),
                    fixCoordIndexing = TRUE, ...) {
 
@@ -149,11 +150,13 @@ setMethod("annotateCircs", signature("RangedSummarizedExperiment"),
             }
 
             # check seqlevel style, match input
-            if (!any(seqlevelsStyle(annot.list$genes) %in%
-                     seqlevelsStyle(se))) {
-              warning("nonmatching seqlevel styles, will fix automatically")
-              for (i in 1:length(annot.list)) {
-                seqlevelsStyle(annot.list[[i]]) <- seqlevelsStyle(se)
+            if (class(try(seqlevelsStyle(se), TRUE)) != "try-error") {
+              if (!any(seqlevelsStyle(annot.list$genes) %in%
+                       seqlevelsStyle(se))) {
+                warning("nonmatching seqlevel styles, will fix automatically")
+                for (i in 1:length(annot.list)) {
+                  seqlevelsStyle(annot.list[[i]]) <- seqlevelsStyle(se)
+                }
               }
             }
 
@@ -200,10 +203,10 @@ annotateHostGenes <- function(se, genes.gr) {
   start(circ.ends.gr) <- end(circ.ends.gr)
 
   olap.start <- findOverlaps(circ.starts.gr, genes.gr, type = "within")
-  olap.end   <- findOverlaps(circ.ends.gr, genes.gr, type = "within")
+  olap.end   <- findOverlaps(circ.ends.gr,   genes.gr, type = "within")
 
-  circs <- data.table(start.hit = names(circs.gr) %in% queryHits(olap.start),
-                      end.hit   = names(circs.gr) %in% queryHits(olap.end),
+  circs <- data.table(start.hit = 1:length(circs.gr) %in% queryHits(olap.start),
+                      end.hit   = 1:length(circs.gr) %in% queryHits(olap.end),
                       id        = circs.gr$id,
                       ord       = 1:length(circs.gr))
 

diff --git a/R/circus.R b/R/circus.R
@@ -11,16 +11,19 @@
 #' @importFrom AnnotationDbi saveDb loadDb
 #' @import AnnotationHub
 #' @importFrom biomaRt useMart useDataset getBM
+#' @importFrom BiocGenerics sort
 #' @importFrom data.table data.table rbindlist dcast.data.table set setnames fread
 #' @import DBI
-#' @importFrom GenomicRanges makeGRangesFromDataFrame resize reduce
+#' @importFrom GenomeInfoDb seqlevelsStyle seqlevelsStyle<- seqlevels<-
+#' @importFrom GenomicRanges makeGRangesFromDataFrame resize reduce GRangesList
 #' @importFrom GenomicFeatures makeTxDbFromGRanges
 #' @import ggplot2
 #' @importFrom hash hash keys
 #' @importFrom IRanges findOverlaps
 #' @import methods
 #' @importFrom RColorBrewer brewer.pal
 #' @import RMySQL
+#' @importFrom rtracklayer export score
 #' @import S4Vectors
 #' @import stringr
 #' @import SummarizedExperiment
@@ -55,6 +58,7 @@ NULL
                            "79"      = "mar2015.archive.ensembl.org",
                            "80"      = "may2015.archive.ensembl.org",
                            "81"      = "jul2015.archive.ensembl.org",
+                           "91"      = "dec2017.archive.ensembl.org",
                            "current" = "ensembl.org"
                            ),
 
@@ -68,8 +72,9 @@ NULL
     assembly2annhub = list("hg19"     = "AH10684",
                            "hg38"     = "AH47963",
                            "mm10"     = "AH47973",
-                           "dm6"      = "AH47953",
+                           "dm6"      = "AH60052",
                            "rn5"      = "AH28841",
+                           "rn6"      = "AH60238",
                            "WBcel235" = "AH47942"
                            ),
 
@@ -78,6 +83,7 @@ NULL
                             "mm10"     = "current",
                             "dm6"      = "current",
                             "rn5"      = "79",
+                            "rn6"      = "91",
                             "WBcel235" = "81"
                             ),