runFrag.R

# file: runFrag.R
# author: Derek Wong, Ph.D
# date: October 5th, 2021

library(optparse)

## Set script variables
option_list <- list(
  make_option(c("--id"), type = "character", help = "sample id. Required"),
  make_option(c("--bamdir"), type = "character", help = "Path to bam files. Required."),
  make_option(c("--filters"), type = "character", help = "Path to genomic blacklist regions. Required."),
  make_option(c("--gaps"), type = "character", help = "Path to genome gaps. Required."),
  make_option(c("--tiles"), type = "character", help = "Path to 100kb tiled genome. Required."),
  make_option(c("--VNTRs"), type = "character", help = "Path to VNTRs. Required."),
  make_option(c("--healthy"), type = "character", help = "Path to panel of healthy controls. Required."),
  make_option(c("--outdir"), type = "character", help = "Path to output directory. Required."),
  make_option(c("--libdir"), type = "character", help = "Path to scripts. Required.")
)
parseobj <- OptionParser(option_list=option_list)
opt <- parse_args(parseobj)
print(opt)
options(scipen=0, stringsAsFactors=F)

## Load required packages
library(tidyverse)
library(multidplyr)
library(Rsamtools)
library(rtracklayer)
library(GenomicAlignments)
library(GenomicRanges)
library(devtools)
library(Homo.sapiens)
library(biovizBase)
library(BSgenome.Hsapiens.UCSC.hg38)
library(readxl)
class(Homo.sapiens)
options(stringsAsFactors=FALSE)
options(bitmapType='cairo')

## Get variables from input script
id <- opt$id
bam <- opt$bam
filters <- opt$filters
gaps <- opt$gaps
tiles <- opt$tiles
VNTRs <- opt$VNTRs
healthy <- opt$healthy
libdir <- opt$libdir
outdir <- file.path(opt$outdir, id)

## Create output directory
dir.create(outdir)

## Run scripts
source(paste0(libdir,"/R/git_01-read_fragments.R"))
source(paste0(libdir,"/R/git_02-mito_frag.R"))
source(paste0(libdir,"/R/git_03-100kb_bins.R"))
source(paste0(libdir,"/R/git_04-5Mb_bins.R"))
source(paste0(libdir,"/R/git_05-summary.R"))
source(paste0(libdir,"/R/git_06-plotting.R"))
#source(paste0(libdir,"/R/git_07-gbm_prediction.R"))

q('no')