From c18793c210ea44cef63db3568791cbad537bdb79 Mon Sep 17 00:00:00 2001 From: Calvin Date: Fri, 8 Mar 2013 15:32:50 -0500 Subject: moving some stuff --- src/quikr | 48 ++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100755 src/quikr (limited to 'src/quikr') diff --git a/src/quikr b/src/quikr new file mode 100755 index 0000000..bac01ca --- /dev/null +++ b/src/quikr @@ -0,0 +1,48 @@ +#!/usr/bin/python +import sys +import os +import argparse +import quikr +import numpy as np + +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.") + + parser.add_argument("-f", "--fasta", help="fasta file", required=True) + parser.add_argument("-o", "--output", help="output path (csv output)", required=True) + parser.add_argument("-t", "--trained-matrix", help="trained matrix", required=True) + parser.add_argument("-l", "--lamb", type=int, help="the default lambda value is 10,000") + parser.add_argument("-k", "--kmer", type=int, required=True, + help="specifies which kmer to use, must be used with a custom trained database") + + + args = parser.parse_args() + + # our default lambda is 10,000 + lamb = 10000 + + # Make sure our input exist + 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") + + # use alternative lambda + if args.lamb is not None: + lamb = args.lamb + + trained_matrix = quikr.load_trained_matrix_from_file(args.trained_matrix) + xstar = quikr.calculate_estimated_frequencies(args.fasta, trained_matrix, args.kmer, lamb) + + np.savetxt(args.output, xstar, delimiter=",", fmt="%f") + return 0 + +if __name__ == "__main__": + sys.exit(main()) -- cgit v1.2.3