bcr_tigger_wrapper.R

#!/opt/conda/bin/Rscript

# Julian Q. Zhou
# https://github.com/julianqz

# wrapper to call run_tigger for a list of individuals from command line via Rscript

# assumes:
# - all input files are in .RData format
# - all input files are in the same pathDb location
# - all input files are named as [prefix]_[subj].RData

suppressPackageStartupMessages(require(optparse))

option_list = list(
    make_option("--pathRunTigger", action="store", default=NA, type="character", 
                help="Path to bcr_tigger.R."),
    make_option("--pathCSV", action="store", default=NA, 
                type="character", help="Path to CSV containing subject list and paths to input files."),
    make_option("--pathIMGT", action="store", default=NA, type="character", 
                help="path_imgt."),
    make_option("--pathHelper", action="store", default=NA, type="character", 
                help="path_helper."),
    make_option("--pathWork", action="store", default=NA, type="character", 
                help="path_work."),
    make_option("--heavyLight", action="store", default=FALSE, 
                type="logical", 
                help="Whether to run separately for both heavy and light chains. Default is heavy only."),
    make_option("--noSplitVersion", action="store", default=FALSE, 
                type="logical", help="no_split_version."),
    make_option("--colSeq", action="store", default="sequence_alignment", 
                type="character", help="col_seq."),
    make_option("--colV", action="store", default="v_call", 
                type="character", help="col_v."),
    make_option("--colProd", action="store", default="productive", 
                type="character", help="col_prod."),
    make_option("--colCDR3Len", action="store", default="cdr3_length", 
                type="character", help="col_cdr3_len."),
    make_option("--findUnmutated", action="store", default=TRUE, 
                type="logical", help="p_find_unmutated."),
    make_option("--textSize", action="store", default=12, 
                type="numeric", help="p_text_size."),
    make_option("--keepGene", action="store", default="gene", 
                type="character", help="p_keep_gene.")
)
opt = parse_args(OptionParser(option_list=option_list))

# without next line sink won't be able to capture tigger version
# (even if func in opt$pathRunTigger `require(tigger)`)
suppressPackageStartupMessages(library(tigger))

# run_tigger()
source(opt$pathRunTigger)

if (opt$heavyLight) {
    run_mode = c("heavy", "light")
} else {
    run_mode = c("heavy")
}

setwd(opt$pathWork)
sinkName = paste0("computingEnv_tigger_", Sys.Date(), "-", 
                  format(Sys.time(), "%H%M%S"), '.txt')
sink(sinkName)
cat("run_mode:", run_mode, "\n")
cat("find_unmutated:", opt$findUnmutated, "\n")
cat("keep_gene:", opt$keepGene, "\n")
sessionInfo()
sink()

subj_info = read.table(opt$pathCSV, header=T, sep=",", stringsAsFactors=F)

# check presence of necessary columns
stopifnot( all( paste0("path_db_", run_mode) %in% colnames(subj_info) ) )

for (i in 1:nrow(subj_info)) {
    
    subj = subj_info[["subj"]][i]

    for (cur_run_mode in run_mode) {
        
        cat("\n", subj, ";", cur_run_mode, "\n")
        
        # db
        cur_col_db = paste0("path_db_", cur_run_mode)
        cur_fn_db = subj_info[[cur_col_db]][i]
        cat(" - loading", cur_fn_db, "\n")
        load(cur_fn_db)
        
        # chain type automatically detected by run_tigger
        run_tigger(path_imgt=opt$pathIMGT, 
                   path_helper=opt$pathHelper, 
                   path_work=opt$pathWork, 
                   subj=subj, db=db, 
                   no_split_version=opt$noSplitVersion,
                   col_seq=opt$colSeq, 
                   col_v=opt$colV, 
                   col_prod=opt$colProd, 
                   col_cdr3_len=opt$colCDR3Len,
                   p_find_unmutated=opt$findUnmutated,
                   p_text_size=opt$textSize,
                   p_keep_gene=opt$keepGene)
    }
}

# prints NULL if none
cat("\nwarnings():\n")
print(warnings())