#!/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)