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Diffstat (limited to 'src/python/quikr.py')
| -rwxr-xr-x | src/python/quikr.py | 6 |
1 files changed, 0 insertions, 6 deletions
diff --git a/src/python/quikr.py b/src/python/quikr.py index 857cd25..1fa27c7 100755 --- a/src/python/quikr.py +++ b/src/python/quikr.py @@ -57,9 +57,6 @@ def train_matrix(input_file_location, kmer): """ input_file = Popen(["bash", "-c", "probabilities-by-read " + str(kmer) + " " + input_file_location + " <(generate_kmers 6)"], stdout=PIPE) - input_file.poll() - if input_file.returncode != 0: - raise ValueError, "probbilties-by-read did not execute properly" # load and normalize the matrix by dividing each element by the sum of it's column. # also do some fancy rotations so that it works properly with quikr @@ -102,9 +99,6 @@ def calculate_estimated_frequencies(input_fasta_location, trained_matrix, kmer, # We use the count program to count count_input = Popen(["count-kmers", "-r", str(kmer), "-1", "-u", input_fasta_location], stdout=PIPE) - count_input.poll() - if count_input.returncode != 0: - raise ValueError, "count-kmers did not execute properly" # load the output of our count program and form a probability vector from the counts counts = np.loadtxt(count_input.stdout) |