tileseqMave: TileSeq MAVE Analysis pipeline

#!/usr/bin/env Rscript

# Copyright (C) 2018  Jochen Weile, Roth Lab
#
# This file is part of tileseqMave.
#
# tileseqMave is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# tileseqMave is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public License
# along with tileseqMave.  If not, see <https://www.gnu.org/licenses/>.

#####################################################
# This is a command line wrapper for buildJointTable
#####################################################

options(
  stringsAsFactors=FALSE,
  ignore.interactive=TRUE,
  future.cmdargs=c()
)

#load libraries
library(tileseqMave)
library(argparser)
library(yogilog)

#process command line arguments
p <- arg_parser(
  "Reads the output of fastq2Count to construct allCounts.csv and marginalCounts.csv",
  name="joinCounts.R"
)
p <- add_argument(p, "--workspace", help="workspace data directory. Defaults to current working directory")
p <- add_argument(p, "--input", help="input directory containing the count data. Defaults to subdirectory with latest timestamp ending in _mut_count")
p <- add_argument(p, "--output", help="output directory. Defaults to same as input directory")
p <- add_argument(p, "--parameters", help="parameter file. Defaults to parameters.json in the workspace directory.")
p <- add_argument(p, "--logfile", help="log file. Defaults to joinCounts.log in the workspace directory")
p <- add_argument(p, "--cores", default=6, help="number of CPU cores to use in parallel for multi-threading")
p <- add_argument(p, "--srOverride", help="Manual override to allow singleton replicates. USE WITH EXTREME CAUTION!",flag=TRUE)
p <- add_argument(p, "--covOverride", help="Manual override to ignore positional coverage. For backwards-compatibility with data prior to v0.7",flag=TRUE)
p <- add_argument(p, "--silent", help="Turn off message printing to stdout",flag=TRUE)
args <- parse_args(p)

#Workaround for bug in future package, that re-uses command line arguments:
#Override commandArgs function with dummy that returns nothing
commandArgs <- function(trailingOnly=FALSE) {
  character()
}

#ensure datadir ends in "/" and exists
dataDir <- args$workspace
if (is.na(dataDir)) {
  dataDir <- getwd()
}
if (!grepl("/$",dataDir)) {
  dataDir <- paste0(dataDir,"/")
}
if (!dir.exists(dataDir)) {
  #logger cannot initialize without dataDirectory, so just a simple exception here.
  stop("Data folder does not exist!")
}
paramfile <- if (is.na(args$parameters)) paste0(dataDir,"parameters.json") else args$parameters
logfile <- if (is.na(args$logfile)) paste0(dataDir,"joinCounts.log") else args$logfile
mc.cores <- if (is.na(args$cores)) 6 else args$cores

#set up logger and shunt it into the error handler
logger <- new.logger(logfile,stdout=!args$silent)
registerLogger(logger)
registerLogErrorHandler(logger)
logVersion()

#run the actual function
invisible(
  buildJointTable(dataDir,inDir=args$input,outDir=args$output,paramfile,
                  mc.cores,srOverride=args$srOverride,covOverride=args$covOverride
  )
)