def create_schema():
def msg(name=None):
return ''' chewBBACA.py CreateSchema [CreateSchema ...] [-h] -i [I] -o [O] --cpu [CPU] [-b [B]] [--bsr [BSR]] [-v] [-l [L]]'''
parser = argparse.ArgumentParser(description="This program creates a schema when provided the genomes",usage=msg())
parser.add_argument('CreateSchema', nargs='+', help='create a schema')
parser.add_argument('-i', nargs='?', type=str, help='List of genome files (list of fasta files)', required=True)
parser.add_argument('-o', nargs='?', type=str, help="Name of the output folder", required=True)
parser.add_argument('--cpu', nargs='?', type=int, help="Number of cpus, if over the maximum uses maximum -2",
required=True)
parser.add_argument('-b', nargs='?', type=str, help="BLAST full path", required=False, default='blastp')
parser.add_argument("--CDS", help="use a fasta file, one gene per entry, to call alleles", required=False, action="store_true", default=False)
parser.add_argument('--bsr', nargs='?', type=float, help="minimum BSR similarity", required=False, default=0.6)
#~ parser.add_argument('-t', nargs='?', type=str, help="taxon", required=False, default=False)
parser.add_argument('--ptf', nargs='?', type=str, help="provide your own prodigal training file (ptf) path", required=False, default=False)
parser.add_argument("-v", "--verbose", help="increase output verbosity", dest='verbose', action="store_true",
default=False)
parser.add_argument('-l', nargs='?', type=int, help="minimum bp locus lenght", required=False, default=201)
args = parser.parse_args()
genomeFiles = args.i
cpuToUse = args.cpu
outputFile = args.o
BlastpPath = args.b
bsr = args.bsr
#~ chosenTaxon = args.t
chosenTrainingFile = args.ptf
verbose = args.verbose
min_length = args.l
inputCDS = args.CDS
if inputCDS==True:
genomeFiles=[os.path.abspath(genomeFiles)]
else:
genomeFiles = check_if_list_or_folder(genomeFiles)
if isinstance(genomeFiles, list):
with open("listGenomes2Call.txt", "w") as f:
for genome in genomeFiles:
f.write(genome + "\n")
genomeFiles = "listGenomes2Call.txt"
PPanGen.main(genomeFiles,cpuToUse,outputFile,bsr,BlastpPath,min_length,verbose,chosenTrainingFile,inputCDS)
try:
os.remove("listGenomes2Call.txt")
except:
pass
def create_schema():
def msg(name=None):
return ''' chewBBACA.py CreateSchema [CreateSchema ...] [-h] -i [I] -o [O] --cpu [CPU] [-b [B]] [--bsr [BSR]] [-v] [-l [L]]'''
parser = argparse.ArgumentParser(description="This program creates a schema when provided the genomes",usage=msg())
parser.add_argument('CreateSchema', nargs='+', help='create a schema')
parser.add_argument('-i', nargs='?', type=str, help='List of genome files (list of fasta files)', required=True)
parser.add_argument('-o', nargs='?', type=str, help="Name of the output folder", required=True)
parser.add_argument('--cpu', nargs='?', type=int, help="Number of cpus, if over the maximum uses maximum -2",
required=True)
parser.add_argument('-b', nargs='?', type=str, help="BLAST full path", required=False, default='blastp')
parser.add_argument("--CDS", help="use a fasta file, one gene per entry, to call alleles", required=False, action="store_true", default=False)
parser.add_argument('--bsr', nargs='?', type=float, help="minimum BSR similarity", required=False, default=0.6)
#~ parser.add_argument('-t', nargs='?', type=str, help="taxon", required=False, default=False)
parser.add_argument('--ptf', nargs='?', type=str, help="provide your own prodigal training file (ptf) path", required=False, default=False)
parser.add_argument("-v", "--verbose", help="increase output verbosity", dest='verbose', action="store_true",
default=False)
parser.add_argument('-l', nargs='?', type=int, help="minimum bp locus lenght", required=False, default=201)
parser.add_argument('--prm', nargs='?', type=str, help="Prodigal run mode. Single or meta. Meta mode is necessary "
"if input genomes/assemblies/plasmids have a total number of base pairs below 20000bp.",
choices=['single', 'meta'], required=False, default='single')
args = parser.parse_args()
genomeFiles = args.i
cpuToUse = args.cpu
outputFile = args.o
BlastpPath = args.b
bsr = args.bsr
#~ chosenTaxon = args.t
chosenTrainingFile = args.ptf
verbose = args.verbose
min_length = args.l
inputCDS = args.CDS
prodigal_mode = args.prm
if inputCDS==True:
genomeFiles=[os.path.abspath(genomeFiles)]
else:
genomeFiles = check_if_list_or_folder(genomeFiles)
if isinstance(genomeFiles, list):
with open("listGenomes2Call.txt", "w") as f:
for genome in genomeFiles:
f.write(genome + "\n")
genomeFiles = "listGenomes2Call.txt"
try:
chosenTrainingFileLocal=os.path.join(os.path.dirname(CHEWBBACA.__file__), "prodigal_training_files",chosenTrainingFile)
except:
chosenTrainingFileLocal=False
pass
if os.path.isfile(chosenTrainingFile):
pass
elif os.path.isfile(chosenTrainingFileLocal):
chosenTrainingFile=chosenTrainingFileLocal
pass
elif not chosenTrainingFileLocal:
pass
else:
print( chosenTrainingFile+ " file not found")
return
PPanGen.main(genomeFiles,cpuToUse,outputFile,bsr,BlastpPath,min_length,verbose,chosenTrainingFile,inputCDS,prodigal_mode)
try:
os.remove("listGenomes2Call.txt")
except:
pass