mirror of
https://github.com/haniffalab/scRNA-seq_analysis.git
synced 2024-10-23 08:29:24 -07:00
69 lines
No EOL
2.2 KiB
R
Executable file
69 lines
No EOL
2.2 KiB
R
Executable file
args = commandArgs(trailingOnly=T)
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args = paste(args, collapse = "")
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args = unlist(strsplit(args, ";"))
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arguments.list = "
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seurat.addr.arg = args[1]
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"
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expected_arguments = unlist(strsplit(arguments.list, "\n"))
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expected_arguments = expected_arguments[!(expected_arguments == "")]
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if(length(args) != length(expected_arguments)){
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error.msg = sprintf('This pipeline requires %s parameters', as.character(length(expected_arguments)))
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expected_arguments = paste(unlist(lapply(strsplit(expected_arguments, ".arg"), "[", 1)), collapse = "\n")
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stop(sprintf('This pipeline requires %s parameters: '))
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}
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eval(parse(text = arguments.list))
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for(n in 1:length(expected_arguments)){
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argument = expected_arguments[n]
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argument = gsub(pattern=" ", replacement="", x=argument)
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argument.name = unlist(strsplit(argument, "="))[1]
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variable.name = gsub(pattern=".arg", replacement="", argument.name)
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argument.content = eval(parse(text = argument.name))
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eval(parse(text = argument.content))
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if (!exists(variable.name)){
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stop(sprintf("Argument %s not passed. Stopping ... ", variable.name))
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}
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}
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# create required folders for output and work material
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output_folder = gsub(pattern="^\\d+_", replacement="", x=basename(getwd()))
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output_folder = paste(output_folder, seurat.addr, sep = "_")
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c.time = Sys.time()
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c.time = gsub(pattern=" BST", replacement="", x=c.time)
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c.time = gsub(pattern=":", replacement="", x=c.time)
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c.time = gsub(pattern=" ", replacement="", x=c.time)
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c.time = gsub(pattern="-", replacement="", x=c.time)
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c.time = substr(x=c.time, start=3, stop=nchar(c.time))
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output_folder = paste(output_folder, c.time, sep = "_")
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output_folder = file.path("../../output", output_folder)
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dir.create(output_folder)
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output_folder_material = file.path(output_folder, "material")
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dir.create(output_folder_material)
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seurat.addr = file.path("../../data", seurat.addr)
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source("../../tools/bunddle_utils.R")
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library(Seurat)
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library(RColorBrewer)
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library(dplyr)
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library(plyr)
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#######################################################################################################
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# load data
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print("loading data ... ")
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seurat.obj = readRDS(seurat.addr)
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print("Data loaded.")
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unlink(output_folder_material, recursive=T, force=T)
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print("Ended beautifully ... ") |