diff options
Diffstat (limited to 'src/python/quikr.py')
| -rwxr-xr-x | src/python/quikr.py | 12 |
1 files changed, 2 insertions, 10 deletions
diff --git a/src/python/quikr.py b/src/python/quikr.py index fe5ea63..802a7e0 100755 --- a/src/python/quikr.py +++ b/src/python/quikr.py @@ -7,7 +7,6 @@ import scipy.sparse import numpy as np from subprocess import * import argparse -import platform import gzip import itertools @@ -100,15 +99,8 @@ def calculate_estimated_frequencies(input_fasta_location, trained_matrix, kmer, species or strain). """ - - uname = platform.uname()[0] - - # We use the count program to count ____ - if uname == "Linux" and os.path.isfile("./count-linux"): - count_input = Popen(["./count-linux", "-r", str(kmer), "-1", "-u", input_fasta_location], stdout=PIPE) - elif uname == "Darwin" and os.path.isfile("./count-osx"): - count_input = Popen(["count-osx", "-r", str(kmer), "-1", "-u", input_fasta_location], stdout=PIPE) - + # We use the count program to count + count_input = Popen(["count-kmers", "-r", str(kmer), "-1", "-u", input_fasta_location], stdout=PIPE) # load the output of our count program and form a probability vector from the counts counts = np.loadtxt(count_input.stdout) |