1. gmapR
  2. R
  3. iit_store-command.R
Browse code

general cleanup and fixes, doc updates

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@111183 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 03/12/2015 21:11:09
Showing 1 changed files
R/iit_store-command.R
History View file @ f053c5f
... ... 
@@ -7,7 +7,8 @@
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 ### High-level wrapper
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 ###
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-setGeneric("iit_store", function(x, dest, BPPARAM=MulticoreParam(1), ...) standardGeneric("iit_store"))
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+setGeneric("iit_store", function(x, dest, BPPARAM=MulticoreParam(1), ...)
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+    standardGeneric("iit_store"))
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 gmapRange <- function(x) {
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   pos <- strand(x) == "+"
... ... 
@@ -28,7 +29,8 @@ gmapRange <- function(x) {
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     strtpos = if(pos) min(strts) else max(ends)
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     endpos = if(!pos) min(strts) else max(ends)
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-    hdr = paste0(">", name, " ", runValue(seqnames(grange))[1], ":", strtpos, "..", endpos )
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+    hdr = paste0(">", name, " ", runValue(seqnames(grange))[1], ":", strtpos,
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+        "..", endpos)
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     datline = paste(name, name, "NA")
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     rngst = if(pos) strts[o] else ends[o]
... ... 
@@ -69,7 +71,7 @@ setMethod("iit_store", c("character"),
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                    label = if (gff) "ID" else NULL)
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           {
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             .iit_store(gff = gff, label = label, sort = "none",
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-                       output = dest, inputfile = x)
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+                       output = dest, .inputfile = x)
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           })
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 ### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Browse code

add codon tally support. No vbump yet

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@93316 bc3139a8-67e5-0310-9ffc-ced21a209358

Gabriel Becker authored on 11/08/2014 23:42:48
Showing 1 changed files
R/iit_store-command.R
History View file @ c78be69
... ... 
@@ -7,7 +7,7 @@
7 7 
 ### High-level wrapper
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 ###
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-setGeneric("iit_store", function(x, dest, ...) standardGeneric("iit_store"))
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+setGeneric("iit_store", function(x, dest, BPPARAM=MulticoreParam(1), ...) standardGeneric("iit_store"))
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 gmapRange <- function(x) {
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   pos <- strand(x) == "+"
... ... 
@@ -18,8 +18,42 @@ gmapRange <- function(x) {
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   range
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 }
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-setMethod("iit_store", c("GenomicRanges", "character"),
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-          function(x, dest, info = colnames(values(x))[1]) {
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+
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+
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+.make_iit_interval = function(grange, name) {
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+    pos = runValue(strand(grange))[1] == "+"
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+    strts = start(grange)
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+    ends = end(grange)
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+    o = order(strts, decreasing = !pos)
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+
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+    strtpos = if(pos) min(strts) else max(ends)
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+    endpos = if(!pos) min(strts) else max(ends)
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+    hdr = paste0(">", name, " ", runValue(seqnames(grange))[1], ":", strtpos, "..", endpos )
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+
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+    datline = paste(name, name, "NA")
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+    rngst = if(pos) strts[o] else ends[o]
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+    rngend = if(!pos) strts[o] else ends[o]
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+    rnglines = paste0(rngst , " ", rngend)
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+    c(hdr, datline, rnglines)
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+}
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+
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+
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+
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+setMethod("iit_store", c("GenomicRangesList"),
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+          function(x, dest =  tempfile(pattern="iit", fileext=".iit"), BPPARAM= MulticoreParam(1)) {
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+              nms = gsub("( |:|\\.)", "_", names(x))
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+              lines = unlist(bpmapply(.make_iit_interval, x, nms, BPPARAM = BPPARAM), use.names = FALSE)
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+              p <- .iit_store(sort = "none", output = dest)
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+              #writeLines(lines, p)
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+              cat(paste(lines, collapse="\n"), file =p)
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+              close(p)
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+              dest
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+          })
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+
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+
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+setMethod("iit_store", c("GenomicRanges"),
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+          function(x, dest =  tempfile(pattern="iit", fileext=".iit"),
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+                   info = colnames(values(x))[1]) {
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             lines <- paste0(">", names(x), " ", gmapRange(x), " ",
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                             values(x)[[info]])
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             p <- .iit_store(sort = "none", output = dest)
... ... 
@@ -28,8 +62,10 @@ setMethod("iit_store", c("GenomicRanges", "character"),
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             dest
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           })
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-setMethod("iit_store", c("character", "character"),
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-          function(x, dest, gff = file_ext(x) == "gff",
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+
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+setMethod("iit_store", c("character"),
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+          function(x, dest =  tempfile(pattern="iit", fileext=".iit"),
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+                   gff = file_ext(x) == "gff",
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                    label = if (gff) "ID" else NULL)
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           {
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             .iit_store(gff = gff, label = label, sort = "none",
Browse code

renaming gmapR2 to gmapR: it lives again

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@68172 bc3139a8-67e5-0310-9ffc-ced21a209358

Michael Lawrence authored on 02/08/2012 22:24:24
Showing 1 changed files
R/iit_store-command.R
History View file @ b22faf0
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,54 @@
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+### =========================================================================
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+### iit_store command
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+### -------------------------------------------------------------------------
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+###
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+
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+### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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+### High-level wrapper
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+###
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+
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+setGeneric("iit_store", function(x, dest, ...) standardGeneric("iit_store"))
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+
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+gmapRange <- function(x) {
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+  pos <- strand(x) == "+"
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+  range <- paste0(seqnames(x), ":", ifelse(pos, start(x), end(x)))
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+  if (!all(width(x) == 1L)) {
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+    range <- paste0(range, "..", ifelse(pos, end(x), start(x)))
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+  }
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+  range
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+}
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+
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+setMethod("iit_store", c("GenomicRanges", "character"),
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+          function(x, dest, info = colnames(values(x))[1]) {
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+            lines <- paste0(">", names(x), " ", gmapRange(x), " ",
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+                            values(x)[[info]])
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+            p <- .iit_store(sort = "none", output = dest)
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+            writeLines(lines, p)
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+            close(p)
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+            dest
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+          })
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+
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+setMethod("iit_store", c("character", "character"),
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+          function(x, dest, gff = file_ext(x) == "gff",
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+                   label = if (gff) "ID" else NULL)
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+          {
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+            .iit_store(gff = gff, label = label, sort = "none",
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+                       output = dest, inputfile = x)
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+          })
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+
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+### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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+### Low-level wrapper
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+###
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+
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+.iit_store <- function(fields = FALSE, gff = FALSE,
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+                       label = if (gff) "ID" else NULL,
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+                       sort = c("chrom", "none", "alpha", "numeric-alpha"),
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+                       output, .inputfile = NULL)
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+{
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+### TODO: assertions
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+  sort <- match.arg(sort)
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+  cl <- commandLine("iit_store")
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+  if (is.null(.inputfile))
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+    pipe(cl, open = "w")
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+  else .system(cl)
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+}