diff --git a/primingsitepredictor/cli.py b/primingsitepredictor/cli.py index cae6bb28680c368d8805d81cb42d22d31fda25dd..0dfcc2a31990247eedeee0b4e712c9a8cde50229 100644 --- a/primingsitepredictor/cli.py +++ b/primingsitepredictor/cli.py @@ -5,17 +5,29 @@ Created on Mon Nov 14 14:49:50 2022 @author: baerma """ import argparse +import logging +def create_parser(): + parser = argparse.ArgumentParser( + prog = 'Priming site predictor', + description = 'Takes a cutoff energy and the predicts location of priming sites of transcripts', + epilog = 'To predict or not to predict') + parser.add_argument('energycutoff', type=float, help='a float as energy Cutoff') + #parser.add_argument('transcripts', help='fastafile containing transcripts') #What type is that? fasta? Actually doesn't make sense here + args = parser.parse_args() + energy_cutoff = args.energycutoff + return energy_cutoff +#possibly make a class out of this although I think it's an overkill -parser = argparse.ArgumentParser(description='Process some integers.') -parser.add_argument('integers', metavar='N', type=int, nargs='+', - help='an integer for the accumulator') -parser.add_argument('--sum', dest='accumulate', action='store_const', - const=sum, default=max, - help='sum the integers (default: find the max)') - -args = parser.parse_args() -print(args.accumulate(args.integers)) - - +def letsgo(): + energy_cutoff = create_parser() + print(f"Your energy cutoff is {energy_cutoff}") +if __name__ == '__main__': + logging.basicConfig( + format='[%(asctime)s: %(levelname)s] %(message)s (module "%(module)s")', + level=logging.INFO, + ) + LOG = logging.getLogger(__name__) + letsgo() + #here we would point to the main module and parse the energy cutoff diff --git a/setup.py b/setup.py index 3120368d0e7db0326010e16d62020496736b3cd4..d86d1a3d6e6cb74dd17ff25a69d20d47a803b5d6 100644 --- a/setup.py +++ b/setup.py @@ -10,6 +10,6 @@ setup( packages = ['primingsitepredictor'], entry_points = { 'console_scripts': [ - 'psp = primingsitepredictor.main:main' + 'primingsitepredictor = primingsitepredictor.cli:letsgo' ] })