#!/usr/bin/env python
"""Test libPoMo.cf.fasta_to_cf with IUPAC codes."""
import os
import libPoMo.cf as cf
######################################################################
print("##################################################")
test_sequence = "data/fasta-iupac.dat"
fn = "vcf-test-tmp.dat"
print("Convert", test_sequence, "to Counts File.")
cf.fasta_to_cf(test_sequence, fn, double_fixed_sites=True)
with open(fn) as file:
for line in file:
print(line, end='')
os.remove(fn)
parser.add_argument("fastaFile",
help="path to (gzipped) fasta file")
parser.add_argument("output",
help="name of (gzipped) outputfile in counts format")
parser.add_argument("-v", "--verbose", action="count",
help="turn on verbosity (-v or -vv)")
parser.add_argument("--iupac", action="store_true",
help="heteorzygotes are encoded with IUPAC codes")
# TODO
# parser.add_argument("-i", "--one-indiv", action="store_true",
# help="randomly choose one indivual per population")
args = parser.parse_args()
FaRefFN = args.fastaFile
output = args.output
vb = args.verbose
iupac_flag = args.iupac
# oneI = args.one_indiv
logging.basicConfig(format='%(levelname)s: %(message)s')
logger = logging.getLogger()
if args.verbose == 0:
logger.setLevel(logging.WARN)
elif args.verbose == 1:
logger.setLevel(logging.INFO)
elif args.verbose == 2:
logger.setLevel(logging.DEBUG)
cf.fasta_to_cf(FaRefFN, output, double_fixed_sites=iupac_flag)
"""
parser = argparse.ArgumentParser(formatter_class=argparse.RawDescriptionHelpFormatter, description=descr)
parser.add_argument("fastaFile", help="path to (gzipped) fasta file")
parser.add_argument("output", help="name of (gzipped) outputfile in counts format")
parser.add_argument("-v", "--verbose", action="count", help="turn on verbosity (-v or -vv)")
parser.add_argument("--iupac", action="store_true", help="heteorzygotes are encoded with IUPAC codes")
# TODO
# parser.add_argument("-i", "--one-indiv", action="store_true",
# help="randomly choose one indivual per population")
args = parser.parse_args()
FaRefFN = args.fastaFile
output = args.output
vb = args.verbose
iupac_flag = args.iupac
# oneI = args.one_indiv
logging.basicConfig(format="%(levelname)s: %(message)s")
logger = logging.getLogger()
if args.verbose == 0:
logger.setLevel(logging.WARN)
elif args.verbose == 1:
logger.setLevel(logging.INFO)
elif args.verbose == 2:
logger.setLevel(logging.DEBUG)
cf.fasta_to_cf(FaRefFN, output, double_fixed_sites=iupac_flag)
#!/usr/bin/env python
"""Test libPoMo.cf.fasta_to_cf with IUPAC codes."""
import os
import libPoMo.cf as cf
######################################################################
print("##################################################")
test_sequence = "data/fasta-iupac.dat"
fn = "vcf-test-tmp.dat"
print("Convert", test_sequence, "to Counts File.")
cf.fasta_to_cf(test_sequence, fn, double_fixed_sites=True)
with open(fn) as file:
for line in file:
print(line, end='')
os.remove(fn)