From 6d656a43639e837067d03ba59665bcfe0d4b87b9 Mon Sep 17 00:00:00 2001 From: mutantturkey Date: Fri, 15 Feb 2013 07:42:12 -0500 Subject: added some comments --- quikr.py | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/quikr.py b/quikr.py index 9cd507c..2c6815c 100644 --- a/quikr.py +++ b/quikr.py @@ -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 -- cgit v1.2.3