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pampa_classify.py

@@ -15,24 +15,29 @@ def main():
                                          usage="pampa_classify [-h]\n   -s SPECTRA \n   -e ERROR \n   -o OUTPUT FILE \n   -p PEPTIDE_TABLE [PEPTIDE_TABLE] | -f FASTA  | -d DIRECTORY\n   [-l LIMIT]\n   [-t TAXONOMY]\n   [-n NEIGHBOURING] [-a]", description="This script is for species identification.")
 
 
-    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) 
-    group2.add_argument("-o", dest="output", help="Output path (should include the output file name)", type=str)
-    group3=parser.add_argument_group('\nOptions for organism selection')
+    group1=parser.add_argument_group('\nMandatory options')
+    group1.add_argument("-s", dest="spectra", help="Path to the spectra files. Authorized formats: cvs, mgd, mzML.", type=str, required=True)
+    group1.add_argument("-e", dest="error", help="Error margin tolerance for the observation (in Dalton or ppm). Recommended values: 0.02 for maldi FT and 0.1 for maldi TOF.", type=float)
+    group1.add_argument("-o", dest="output", help="Output path (should include the output file name)", type=str)
+    group2=parser.add_argument_group('\nSelection of organisms, basic usage')
+    group2.add_argument("--mammals", help="use pre-computed peptide table and taxonomy for mammals.", action='store_true')
+    group3=parser.add_argument_group('\nSelection of organisms, advanced usage')
     group3.add_argument("-p", dest="peptide_table",nargs='+', help="Peptide table(s) (TSV file(s))", type=str)
     group3.add_argument("-f", dest="fasta", help="Fasta sequences", type=str)
     group3.add_argument("-d", dest="directory",  help="Directory where to find  Fasta files.", type=str)
-    group3.add_argument("-l", dest="limit",  help="Limit the set of peptides or fasta sequences to organisms, molecules or sequence ID specified in this file  (TSV files)", type=str, required=False)
     group3.add_argument("-t", dest="taxonomy", help="Taxonomy (TSV file), optional.", type=str)
-    group4=parser.add_argument_group('\nOptions for suboptimal solutions')
-    group4.add_argument("-n", dest="neighbour", help="Provide near-optimal solutions within a specified percentage margin, ranging between 0 and 100. Default is 100. With -n 100, only optimal solutions are provided.", type=int, required=False, default=100)
-    group4.add_argument("-a", dest="all", action='store_true', help="Provide all solutions within the percentage margin specified with option  -n, and not only suboptimal solutions.  Default is False.", required=False)  
-    group4.add_argument("--web", dest="web",  action='store_true', help=argparse.SUPPRESS, required=False)
+    group4=parser.add_argument_group('\nOptions to limit peptide markers')
+    group4.add_argument("-l", dest="limit",  help="Limit the set of peptides or fasta sequences to organisms, molecules or sequence ID specified in this file (TXT file)", type=str, required=False)
+    group5=parser.add_argument_group('\nApplying deamidation')
+    group5.add_argument("--deamidation", dest="deamidation",  help="Apply deamidation to peptide markers. Can be used in conjunction with the -l option to specify the list of peptide markers to process. By default, all markers are processed.", action='store_true', required=False)
+    group6=parser.add_argument_group('\nOptions for suboptimal solutions')
+    group6.add_argument("-n", dest="neighbour", help="Provide near-optimal solutions within a specified percentage margin, ranging between 0 and 100. Default is 100. With -n 100, only optimal solutions are provided.", type=int, required=False, default=100)
+    group6.add_argument("-a", dest="all", action='store_true', help="Provide all solutions within the percentage margin specified with option  -n, and not only suboptimal solutions.  Default is False.", required=False, default=False)
+    group6.add_argument("--web", dest="web",  action='store_true', help=argparse.SUPPRESS, required=False)
     
     args = parser.parse_args()
     
-    classify.main(args.spectra, args.taxonomy, args.peptide_table, args.fasta, args.directory, args.limit, args.error, args.neighbour, args.all, args.output,None, False, args.web)
+    classify.main(args.spectra,  args.taxonomy, args.peptide_table, args.fasta, args.directory, args.limit, args.deamidation, args.error, args.neighbour, args.all, args.output,args.mammals, args.web)
  
 if __name__ == "__main__":
     main()