diff --git a/scripts/argparse_example.py b/scripts/argparse_example.py new file mode 100644 index 0000000000000000000000000000000000000000..7068aaa74053f54baef7e06a8c7aeb1bb5a898cc --- /dev/null +++ b/scripts/argparse_example.py @@ -0,0 +1,31 @@ +import argparse + +if __name__ == '__main__': + parser = argparse.ArgumentParser( + description="transcript sampler", + formatter_class=argparse.ArgumentDefaultsHelpFormatter + ) + parser.add_argument("--annotation", required=True, help="gtf file with genome annotation") + parser.add_argument("--expression_level", required=True, help="csv file with expression level") + parser.add_argument("--output_csv", required=True, help="output csv file") + parser.add_argument("--output_gtf", required=True, help="output gtf file") + parser.add_argument("--transcript_number", required=True, help="total number of transcripts to sample") + args = parser.parse_args() + + + +# script name being whatever we call our workflow class/function that takes the inputs + script_name(args.annotation, args.expression_level, args.output_csv, args.output_gtf, args.transcript_number) + + +"""note: +so to run our entire workflow, it will suffice to type the following into the command line: + python filename.py \ + --annotation filename1.gtf \ + --expression_level filename2.gtf \ + --output_csv output1.csv \ + --output_gtf output2.gtf \ + --transcript_number 100 (some number) + + +""" \ No newline at end of file