From 3631a0c9d47d8ff72085bcc534bd24bfad4f73da Mon Sep 17 00:00:00 2001 From: Calvin Date: Tue, 14 May 2013 19:50:28 -0400 Subject: use sensing matrix --- src/python/quikr | 16 ++++++---------- 1 file changed, 6 insertions(+), 10 deletions(-) (limited to 'src/python/quikr') diff --git a/src/python/quikr b/src/python/quikr index bae2b9f..7c9ce25 100755 --- a/src/python/quikr +++ b/src/python/quikr @@ -9,15 +9,11 @@ def main(): parser = argparse.ArgumentParser(description= "Quikr returns the estimated frequencies of batcteria present when given a \ - 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.") - + input FASTA file. \n") parser.add_argument("-f", "--fasta", help="the sample's fasta file of NGS READS", required=True) parser.add_argument("-o", "--output", help="OTU_FRACTION_PRESENT, a vector \ representing the percentage of database sequence's presence in a sequence. (csv output)", required=True) - parser.add_argument("-t", "--trained-matrix", help="the trained matrix", required=True) + parser.add_argument("-s", "--sensing-matrix", help="the sensing matrix", required=True) parser.add_argument("-l", "--lamb", type=int, help="the lambda size. (default is 10,000") parser.add_argument("-k", "--kmer", type=int, required=True, help="specifies the size of the kmer to use (the default is 6)") @@ -33,8 +29,8 @@ def main(): if not os.path.isfile(args.fasta): parser.error( "Input fasta file not found") - if not os.path.isfile(args.trained_matrix): - parser.error("Custom trained matrix not found") + if not os.path.isfile(args.sensing_matrix): + parser.error("Custom sensing matrix not found") # use alternative lambda if args.lamb is not None: @@ -44,8 +40,8 @@ def main(): if args.kmer is not None: kmer = args.kmer - trained_matrix = quikr.load_trained_matrix_from_file(args.trained_matrix) - xstar = quikr.calculate_estimated_frequencies(args.fasta, trained_matrix, kmer, lamb) + sensing_matrix = quikr.load_sensing_matrix_from_file(args.sensing_matrix) + xstar = quikr.calculate_estimated_frequencies(args.fasta, sensing_matrix, kmer, lamb) np.savetxt(args.output, xstar, delimiter=",", fmt="%f") return 0 -- cgit v1.2.3