Delete pampa_light.py

pampa_light.py

-"""
-pampa_ligth.py
-
-light version of pampa:
-assignment with preset options, coming with predefined peptide tables and predefined taxonomies
-
-"""
-
-#!/usr/bin/env python3
-
-import argparse
-from src import classify
-
-
-def main():
-    parser = argparse.ArgumentParser(usage="\n \n pampa_light [-h] <general options> <preset options for organism selection> <non-mandatory advanced options>")
-    group2=parser.add_argument_group('\ngeneral options')
-    group2.add_argument("-s", dest="spectra", help="Path to the spectra files (one spectrum per file). Authorized formats: cvs, mgd, mzML.", type=str, required=True)
-    group2.add_argument("-e", dest="error", help="Maximal error margin for the observation (in Dalton or ppm). Recommended values: 0.02 for maldi FT and 0.1 for maldi TOF.", type=float, required=True) 
-    group2.add_argument("-o", dest="output", help="Output path (should include the output file name)", type=str, required=True)
-
-    group = parser.add_argument_group('preset options for organism selection')
-    group.add_argument("--mammals", help="use pre-computed peptide table and taxonomy for mammals.", action='store_true')
-
-    group3=parser.add_argument_group('\nnon-mandatory advanced options')
-    group3.add_argument("-l", dest="limit",  help="Limit the set of markers to organisms, molecules or sequence ID specified in this file  (TXT files)", type=str, required=False)
-    group3.add_argument("-n", dest="neighbour", help="Also provide near-optimal solutions within a specified percentage margin, ranging between 0 and 100. Default is 100. Only suboptimal solutions are provided.", type=int, required=False, default=100)
-    group3.add_argument("-a", dest="all", action='store_true', help="Provide all solutions, and not only suboptimal solutions, within the percentage margin specified with parameter -n. Default is False.", required=False)  
-  
-    args = parser.parse_args()
-
-    classify.main(args.spectra, None, None, None, None, args.limit, args.error, args.neighbour, args.all, args.output, args.mammals, True, False)  
-    
-if __name__ == "__main__":
-    main()