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December 24, 2015 08:39
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Proof of concept for a wrapper for ShortRead::FastqStreamer that preloads the next set of reads while the calling code is processing the previous set.
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library(ShortRead) | |
library(parallel) | |
tsmsg <- function(...) message(format(Sys.time(), "%Y-%m-%d %H:%M:%OS6"), ": ", ...) | |
## Like readChild but returns NULL when child is finished, and | |
## automatically unserializes results. | |
readChildSafe <- function(child) { | |
res <- parallel:::readChild(child) | |
if (is.integer(res) || is.null(res)) { | |
return(NULL) | |
} | |
return(unserialize(res)) | |
} | |
.PreloadProcWrapper <- setClass("PreloadProcWrapper", slots=c(proc="ANY")) | |
setValidity("PreloadProcWrapper", function(object) { | |
if (is(object@proc, "process")) | |
TRUE | |
else | |
"proc must be a process" | |
}) | |
PreloadProcWrapper <- function(proc) .PreloadProcWrapper(proc=proc) | |
setMethod("yield", signature=c(x="PreloadProcWrapper"), definition = function(x, ...) { | |
parallel:::sendChildStdin(x@proc, "\n") | |
readChildSafe(x@proc) | |
}) | |
## returns a function that works like the constructor function but | |
## transparently preloads. | |
preloadWrapper <- function(constructor, yieldMethod) { | |
function(...) { | |
args <- list(...) | |
proc <- mcparallel({ | |
stream <- do.call(constructor, args) | |
nyield <- 0 | |
while (length(nextYield <- yieldMethod(stream))) { | |
nyield <- nyield + 1 | |
tsmsg("CHILD: Preloaded yield ", nyield, ".") | |
## Wait for the next request | |
readLines(con=stdin(), n=1) | |
parallel:::sendMaster(nextYield) | |
tsmsg("CHILD: Sent yield ", nyield, ".") | |
} | |
NULL | |
}) | |
PreloadProcWrapper(proc) | |
} | |
} | |
PreloadingFastqStreamer <- preloadWrapper(FastqStreamer, yield) | |
{ | |
sp <- SolexaPath(system.file('extdata', package='ShortRead')) | |
fl <- file.path(analysisPath(sp), "s_1_sequence.txt") | |
fqs <- PreloadingFastqStreamer(fl, n=50) | |
Sys.sleep(1) | |
nyield <- 0 | |
tsmsg("MAIN: Requesting yield ", nyield+1, ".") | |
while(length(x <- yield(fqs))) { | |
nyield <- nyield + 1 | |
tsmsg("MAIN: Received yield ", nyield, ".") | |
# Long calculation here | |
Sys.sleep(1) | |
tsmsg("MAIN: Processed yield ", nyield, ".") | |
tsmsg("MAIN: Requesting yield ", nyield+1, ".") | |
} | |
} |
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