diff options
| -rw-r--r-- | quikr.py | 8 |
1 files changed, 3 insertions, 5 deletions
@@ -11,10 +11,10 @@ def main(): parser = argparse.ArgumentParser(description= "Quikr returns the estimated frequencies of batcteria present when given a \ - input FASTA file. \n \ + input FASTA file. \n \ A default trained matrix will be used if none is supplied \n \ You must supply a kmer and default lambda if using a custom trained \ - matrix. ") + matrix.") parser.add_argument("-f", "--fasta", help="path to a fasta file", required=True) parser.add_argument("-t", "--trained-matrix", help="path to a custom trained matrix") @@ -30,8 +30,6 @@ def main(): if not os.path.isfile(args.fasta): parser.error( "Input fasta file not found") - - # If we are using a custom trained matrix, we need to do some basic checks if args.trained is not None: @@ -43,7 +41,7 @@ def main(): if args.lamb is None: # use 10,000 as default Lambda input_lambda = 10000 - + # If we aren't using a custom trained matrix, load in the defaults else: trained_matrix_location = "trainset7_112011N6Aaux.mat" input_lambda = 10000 |