def main():
parser = argparse.ArgumentParser(
prog="SC_Mutation",
description=
"Analyze Mutational properites of Single Cell RNA-seq data",
epilog='Enjoy the program! :)')
parser.add_argument("-A",
"--annovar",
help="run annovar on my project",
dest='function_ann',
action='store_true')
parser.add_argument("-cb",
"--cbsniffer",
help="Run CbSniffer on the genes",
dest='function_cbs',
action='store_true')
parser.add_argument("-eg",
"--extract_genes",
help="extract the giver gene list",
dest='function_eg',
action='store_true')
parser.add_argument("project",
help="the project to run these on ",
type=str)
parser.add_argument("-gi",
help="the gene list input to extract ",
type=str,
action='store',
required=False)
parser.add_argument(
"-vc",
help="run variant calling, please choose your tool : Samtools, GATK ",
type=str,
action='store',
required=False)
parser.add_argument("-sb",
"--split-bam",
help="Split bamfile with cell barcodes",
dest='spliter',
action='store_true')
args = parser.parse_args()
gene_list = []
if args.gi:
gene_list = [line.rstrip('\n') for line in open("genelist")]
project = args.project
root = "/home/aiden/gary/Projects/"
log = open("pipeline.txt", "w+")
proc = Process(project,
gene_list,
log,
annovar=args.function_ann,
cbsniffer=args.function_cbs,
extract_genes=args.function_eg)
if args.vc:
caller = args.vc
call = VariantCaller(project, caller, log)
if caller == "Samtools":
call.Samtools()
elif caller == "GATK":
call.GATK()
if args.spliter:
proc.split_Cells()
proc.Annovar()
proc.Extract_genes()
proc.Cb_sniffer()
