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)
