diff options
| -rwxr-xr-x | quikr_train.py | 9 |
1 files changed, 4 insertions, 5 deletions
diff --git a/quikr_train.py b/quikr_train.py index 6415f67..6534b6f 100755 --- a/quikr_train.py +++ b/quikr_train.py @@ -16,9 +16,9 @@ def main(): " quikr_train returns a custom trained matrix that can be used with \ the quikr function. \n You must supply a kmer. \n ") - parser.add_argument("-i", "--input", help="path to the database", required=True) - parser.add_argument("-o", "--output", help="path to output", required=True) - parser.add_argument("-k", "--kmer", type=int, help="specifies which kmer to use", required=True) + parser.add_argument("-i", "--input", help="training database of sequences (fasta format)", required=True) + parser.add_argument("-o", "--output", help="sensing matrix (text file)", required=True) + parser.add_argument("-k", "--kmer", type=int, help="kmer size (integer)", required=False, dtype=int) args = parser.parse_args() @@ -29,7 +29,6 @@ def main(): matrix = quikr_train(args.input, args.kmer) np.save(args.output, matrix) - np.savetxt("python.csv", matrix, delimiter=",") return 0 @@ -41,7 +40,7 @@ def quikr_train(input_file_location, kmer): kmer_file_name = str(kmer) + "mers.txt" if not os.path.isfile(kmer_file_name): - print "could not find kmer file" + print "could not find kmer file" exit() |