Mercurial > repos > iuc > iedb_api

comparison iedb_api.py @ 1:6cf84410cb2e draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/iedb_api commit 848c47fb29e9f1d319056a94a7dbd90129a4aafc"
author iuc
date Tue, 07 Apr 2020 23:20:35 -0400
parents fe3c43451319
children e95d3221b7f0
comparison
equal deleted inserted replaced
0:fe3c43451319 1:6cf84410cb2e
25 prediction_methods = {'mhci': mhci_methods, 25 prediction_methods = {'mhci': mhci_methods,
26 'mhcii': mhcii_methods, 26 'mhcii': mhcii_methods,
27 'processing': processing_methods, 27 'processing': processing_methods,
28 'mhcnp': mhcnp_methods, 28 'mhcnp': mhcnp_methods,
29 'bcell': bcell_methods} 29 'bcell': bcell_methods}
30 all_methods = set(mhci_methods + mhcii_methods + 30 all_methods = set(mhci_methods + mhcii_methods + mhcnp_methods + bcell_methods)
31 mhcnp_methods + bcell_methods)
32 prediction_lengths = {'mhci': range(8, 16), 31 prediction_lengths = {'mhci': range(8, 16),
33 'mhcii': range(11, 31), 32 'mhcii': range(11, 31),
34 'processing': range(8, 15), 33 'processing': range(8, 15),
35 'mhcnp': range(8, 12), 34 'mhcnp': range(8, 12),
36 'bcell': range(8, 16)} 35 'bcell': range(8, 16)}
156 default=None, 155 default=None,
157 help='File of HLA alleles') 156 help='File of HLA alleles')
158 parser.add_argument('-l', '--length', 157 parser.add_argument('-l', '--length',
159 action="append", 158 action="append",
160 default=[], 159 default=[],
161 help='lengths for which to make predictions, ' + 160 help='lengths for which to make predictions, '
162 '1 per allele') 161 '1 per allele')
163 parser.add_argument('-w', '--window_size', 162 parser.add_argument('-w', '--window_size',
164 type=int, 163 type=int,
165 default=None, 164 default=None,
166 help='window_size for bcell prediction') 165 help='window_size for bcell prediction')
167 parser.add_argument('-i', '--input', 166 parser.add_argument('-i', '--input',
168 default=None, 167 default=None,
169 help='Input file for peptide sequences ' + 168 help='Input file for peptide sequences '
170 '(fasta or tabular)') 169 '(fasta or tabular)')
171 parser.add_argument('-c', '--column', 170 parser.add_argument('-c', '--column',
172 default=None, 171 default=None,
173 help='Peptide Column in a tabular input file') 172 help='Peptide Column in a tabular input file')
174 parser.add_argument('-C', '--id_column', 173 parser.add_argument('-C', '--id_column',
203 if args.prediction != 'bcell': 202 if args.prediction != 'bcell':
204 if not args.allele and not args.allelefile: 203 if not args.allele and not args.allelefile:
205 warn_err('-a allele or -A allelefile required\n', exit_code=1) 204 warn_err('-a allele or -A allelefile required\n', exit_code=1)
206 205
207 if not (args.sequence or args.input): 206 if not (args.sequence or args.input):
208 warn_err('NO Sequences given: ' + 207 warn_err('NO Sequences given: '
209 'either -s sequence or -i input_file is required\n', 208 'either -s sequence or -i input_file is required\n',
210 exit_code=1) 209 exit_code=1)
211 210
212 if args.output is not None: 211 if args.output is not None:
213 try: 212 try: