From 3f0c33ff93dea10b2f79c8c2101431e251b8b928 Mon Sep 17 00:00:00 2001 From: Calvin Date: Mon, 11 Mar 2013 12:40:47 -0400 Subject: move python stuff to python directory --- src/quikr | 48 ------------------------------------------------ 1 file changed, 48 deletions(-) delete mode 100755 src/quikr (limited to 'src/quikr') diff --git a/src/quikr b/src/quikr deleted file mode 100755 index bac01ca..0000000 --- a/src/quikr +++ /dev/null @@ -1,48 +0,0 @@ -#!/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