PING/PING_run_all.R at master · patidarr/PING · GitHub

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#!/usr/bin/env Rscript
# Copyright 2016 Wesley Marin, Jill Hollenbach, Paul Norman
#
# This file is part of PING.
#
# PING is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# PING 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 General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with PING.  If not, see <http://www.gnu.org/licenses/>.

suppressPackageStartupMessages(library("optparse"))
suppressPackageStartupMessages(library("data.table"))
option_list <- list(
		make_option("--threads", help="Number of threads"),
		make_option("--location",help="Directory Location where fastq files are stored"),
		make_option("--R1", help="Fastq File Read 1 Pattern"),
		make_option("--R2", help="Fastq File Read 2 Pattern"),
		make_option("--out", help="directory where to write output")
)
opt <- parse_args(OptionParser(option_list=option_list))

bowtie.threads =opt$threads
sample.location=opt$location
fastq.pattern.1=opt$R1
fastq.pattern.2=opt$R2
results.directory=opt$out


source("PING_allele_caller_v1.0.R")
source("PING_extractor_v1.0.R")
source("PING_gc_caller_v1.1.R")


# Creates results directory
#results_directory <- function() {
#	cat("----- Getting PING ready -----\n\n")
#	if(results.directory != ""){
#		save_to <- results.directory
#	}else{
#		save_to <- paste0("All_results_", format(Sys.time(), "%Y_%m_%d_%H:%M"), "/")
#		count <- 1
#		while(file.exists(save_to)) {
#			save_to <- paste0("All_results_", format(Sys.time(), "%Y_%m_%d_%H:%M"), "_", count, "/")
#			count <- count + 1
#		}
#	}
#	dir.create(save_to)
#	cat(paste("Results being saved to", save_to, "\n\n"))
#	return(save_to)
#}
if(dir.exists(results.directory) == 'FALSE'){
	dir.create(results.directory)
}

ping_extractor(sample.location = sample.location,
		fastq.pattern.1 = fastq.pattern.1,
		fastq.pattern.2 = fastq.pattern.2,
		bowtie.threads = bowtie.threads,
		results.directory=paste0(results.directory,"/PING_sequences/")
	)

sample.location <- paste(results.directory,"/PING_sequences/")

is_gz <- last(unlist(strsplit(fastq.pattern.1, ".", fixed = T))) == "gz"

if(is_gz){
	fastq.pattern.1 <- "_1.fastq.gz"
	fastq.pattern.2 <- "_2.fastq.gz"
}else{
	fastq.pattern.1 <- "_1.fastq"
	fastq.pattern.2 <- "_2.fastq"
}

ping_gc_caller(sample.location = sample.location, results.directory = results.directory, read.cap = 40000)

ping_gc_output <- paste0(results.directory, "Combined_results.csv")

ping_allele_caller(sample.location = sample.location,
		fastq.pattern.1 = fastq.pattern.1,
		fastq.pattern.2 = fastq.pattern.2,
		bowtie.threads = bowtie.threads,
		ping.gc.output = ping_gc_output,
		results.directory = results.directory
)