def shuffleVector(vectorS): vlen = len(vectorS) portionToShuffle = int(ShufflePortion * vlen) tempVec = list(vectorS) if (portionToShuffle < 1): raise CF.InputError("Given portion to shuffle is less than 1.") else: random.seed(dt.now().time()) portionIndex = random.sample(range(0, vlen), portionToShuffle) shuffleV = list(np.array(vectorS)[portionIndex]) random.shuffle(shuffleV) for i in range(0, len(portionIndex)): tempVec[portionIndex[i]] = shuffleV[i] return tempVec
#Optional Arguments: parser.add_argument('-t', '--FIX_THRESHOLD', help='User defined fixation cut-off. Default = 0.75', type=float) if (len(sys.argv) <= 1): print(program_function) parser.print_help() sys.exit() args = parser.parse_args() #Checking Required Arguments: if (not CF.okFile(args.SNP_FILE)): raise CF.InputError(args.SNP_FILE, "Invalid input file: ") if (not CF.okFile(args.REF_SEQ)): raise CF.InputError(args.REF_SEQ, "Invalid input file: ") else: ref_record = CF.getFile(args.REF_SEQ) CF.recordCheck(ref_record, args.REF_SEQ) ref_record = CF.getFile( args.REF_SEQ ) #reparse the reference file, because iterator does not reset. #Checking Optional Arguments: if (args.FIX_THRESHOLD): CutOff = args.FIX_THRESHOLD subFixation(ref_record, args.SNP_FILE)
parser.add_argument('-extra', '--EXTRA_FILES', help = 'Prevents removal of potentially useful output files that iedb_tool.py makes.', action = 'store_true' ) parser.add_argument('-mfile', '--IEDB_MPRED', help = 'Parsed prediction file of mutated epitopes from iedbPredictionParser.') parser.add_argument('-mref', '--MUT_SEQ', help = 'A fasta sequence file in amino acids with mutations subbed in. Output of fixationSubber.py') parser.add_argument('-n', '--OUT_NAME', help = 'Prefix to add to output file name. Otherwise names files with default prefix "Result"') if(len(sys.argv) <= 1): print(program_function) parser.print_help() sys.exit() args = parser.parse_args() #Checking Required Arguments: if(not CF.okFile(args.IEDB_CSV)): raise CF.InputError(args.IEDB_CSV, "Invalid input file: ") if(not CF.okFile(args.IEDB_PRED)): raise CF.InputError(args.IEDB_PRED, "Invalid input file: ") if(not CF.okFile(args.HLA_LIST)): raise CF.InputError(args.HLA_LIST, "Invalid input file: ") #Checking Optional Arguments: if(args.R_LIST): if(not CF.okFile(args.R_LIST)): raise CF.InputError(args.R_LIST, "Invalid input file: ") if(args.H_VALUE): HomologyFloat = args.H_VALUE if(args.OUT_DIR): if(os.path.isdir(args.OUT_DIR)): WriteDIR = args.OUT_DIR + '/' else:
type=float) parser.add_argument( '-upper', '--ranking_threshold_upper', help= 'Cut off of epitopes at a defined percentile ranking (Range 0-100). Default = 0.0', type=float) if (len(sys.argv) <= 1): print(program_function) parser.print_help() sys.exit() args = parser.parse_args() #Checking Required Arguments if (not CF.okFile(args.IEDB_prediction)): raise CF.InputError(args.IEDB_prediction, "Invalid input file: ") OutputPath = args.output_name #Checking Optional Arguments if (args.ranking_threshold_lower): RankingCutOffLower = args.ranking_threshold_lower if (args.ranking_threshold_upper): RankingCutOffUpper = args.ranking_threshold_upper (patternHash, HLA_Set) = parse_iedb_rec(args.IEDB_prediction, RankingCutOffLower, RankingCutOffUpper) outputHash(patternHash) outputHLA(HLA_Set)