git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@111240 bc3139a8-67e5-0310-9ffc-ced21a209358
Michael Lawrence authored on 05/12/2015 15:00:00
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@@ -47,7 +47,7 @@ setMethod("gmap", c("character", "GmapParam"),
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| 47 | 47 |
output_path <- output_dir |
| 48 | 48 |
} else {
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output_path <- paste0(output, ".", |
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- formatToExt(params$format)) |
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+ formatToExt(params_list$format)) |
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params_list$.redirect <- paste(">", output_path)
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} |
| 53 | 53 |
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git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/gmapR@110840 bc3139a8-67e5-0310-9ffc-ced21a209358
Michael Lawrence authored on 23/11/2015 23:25:34
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@@ -6,6 +6,133 @@ |
| 6 | 6 |
### High-level interface |
| 7 | 7 |
### |
| 8 | 8 |
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+setGeneric("gmap", function(input, params, ...) standardGeneric("gmap"))
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+ |
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+setMethod("gmap", c("ANY", "GmapParam"),
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+ function(input, params, ...) {
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+ tmpfile <- tempfile() |
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+ export(input, tmpfile, format="fasta") |
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+ input <- tmpfile |
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+ callGeneric() |
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+ }) |
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+ |
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+setMethod("gmap", c("FastaFile", "GmapParam"),
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+ function(input, params, ...) {
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+ input <- path(input) |
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+ callGeneric() |
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+ }) |
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+ |
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+setMethod("gmap", c("character", "GmapParam"),
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+ function(input, params, |
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+ output = file.path(getwd(), |
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+ file_path_sans_ext(basename(input), TRUE)), ...) |
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+ {
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+ if (any(is.na(input))) |
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+ stop("'input' must not contain NA's")
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+ if (length(input) > 1L) {
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+ return(GmapOutputList(mapply(gmap, input, |
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+ MoreArgs = |
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+ list(params, output, |
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+ ...)))) |
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+ } |
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+ |
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+ output_dir <- dirname(output) |
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+ if (!file.exists(output_dir)) |
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+ dir.create(output_dir, recursive = TRUE) |
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+ |
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+ params <- initialize(params, ...) |
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+ params_list <- as.list(params) |
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+ if (gsnap_split_output(params)) {
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+ params_list$split_output <- output |
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+ output_path <- output_dir |
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+ } else {
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+ output_path <- paste0(output, ".", |
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+ formatToExt(params$format)) |
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+ params_list$.redirect <- paste(">", output_path)
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+ } |
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+ |
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+ res <- do.call(.gmap, |
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+ c(list(.input = input), params_list)) |
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+ gmap_output<- GmapOutput(path = output_path, |
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+ version = gmapVersion(), |
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+ param = params) |
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+ |
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+ if (params_list$format %in% c("samse", "sampe")) {
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+ gmap_output <- asBam(gmap_output) |
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+ } |
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+ gmap_output |
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+ }) |
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+ |
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### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
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### Low-level interface |
| 11 | 68 |
### |
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+ |
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+.gmap <- function(db = NULL, dir = NULL, |
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+ kmer = NULL, basesize = NULL, sampling = NULL, |
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+ genomefull = FALSE, gseg = NULL, |
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+ selfalign = FALSE, pairalign = FALSE, |
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+ part = NULL, input_buffer_size = 1000L, |
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+ batch = c("0", "1", "2", "3", "4", "5"),
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+ expand_offsets = FALSE, nosplicing = FALSE, |
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+ min_intronlength = 9L, intronlength = 1000000L, |
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+ localsplicedist = 2000000L, totallength = 2400000L, |
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+ chimera_margin = 40L, no_chimeras = FALSE, |
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+ nthreads = NULL, chrsubsetfile = NULL, |
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+ direction = c("auto", "sense_force", "antisense_force",
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+ "sense_filter", "antisense_filter"), |
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+ trimendexons = 12L, canonical_mode = c("1", "0", "2"),
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+ cross_species = FALSE, allow_close_indels = c("1", "0", "2"),
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+ microexon_spliceprob = 0.90, cmetdir = NULL, atoidir = NULL, |
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+ mode = c("standard", "cmet-stranded", "cmet-nonstranded",
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+ "atoi-stranded", "atoi-nonstranded"), |
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+ prunelevel = c("0", "1", "2", "3"),
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+ format = NULL, npaths = 5L, quiet_if_excessive = FALSE, |
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+ suboptimal_score = NULL, ordered = FALSE, md5 = FALSE, |
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+ chimera_overlap = FALSE, failsonly = FALSE, nofails = FALSE, |
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+ fails_as_input = FALSE, snpsdir = NULL, use_snps = NULL, |
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+ split_output = NULL, append_output = FALSE, |
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+ output_buffer_size = 1000L, fulllength = FALSE, |
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+ cdsstart = NULL, truncate = FALSE, tolerant = FALSE, |
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+ no_sam_headers = FALSE, sam_use_0M = FALSE, |
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+ force_xs_dir = FALSE, md_lowercase_snp = FALSE, |
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+ read_group_id = NULL, read_group_name = NULL, |
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+ read_group_library = NULL, read_group_platform = NULL, |
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+ quality_protocol = c("sanger", "illumina"),
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+ quality_print_shift = 0L, mapdir = NULL, map = NULL, |
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+ mapexons = FALSE, mapboth = FALSE, version = FALSE, |
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+ .input = NULL, .redirect = NULL) |
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+{
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+ formals <- formals(sys.function()) |
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+ |
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+ expand_offsets <- as.integer(expand_offsets) |
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+ batch <- match.arg(batch) |
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+ direction <- match.arg(direction) |
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+ canonical_mode <- match.arg(canonical_mode) |
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+ allow_close_indels <- match.arg(allow_close_indels) |
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+ mode <- match.arg(mode) |
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+ prunelevel <- match.arg(prunelevel) |
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+ quality_protocol <- match.arg(quality_protocol) |
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+ |
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+ if (version) {
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+ .redirect <- ">/dev/null" |
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+ } |
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+ |
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+### TODO: if input_a is NULL, or split_output and .redirect are NULL: |
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+### return a pipe() |
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+ .system_gsnap(commandLine("gmap"))
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+} |
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+ |
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+..gmap <- function(args, path = NULL) {
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+ .system_gsnap(.commandLine("gmap", args, path))
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+} |
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+ |
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+### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
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+### Utilities |
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+### |
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+ |
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+gmapVersion <- function() {
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+ output <- .gmap(version = TRUE) |
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+ version_text <- sub("GMAP version (.*?) .*", "\\1", output[1])
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+ parseGsnapVersion(version_text) |
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+} |
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+ |
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
| 1 | 1 |
new file mode 100644 |
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@@ -0,0 +1,11 @@ |
| 1 |
+### ========================================================================= |
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+### gmap command |
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+### ------------------------------------------------------------------------- |
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+ |
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+### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
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+### High-level interface |
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+### |
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+ |
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+### - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
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+### Low-level interface |
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+### |