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Diffstat (limited to 'src')
| -rwxr-xr-x | src/python/quikr.py | 7 |
1 files changed, 7 insertions, 0 deletions
diff --git a/src/python/quikr.py b/src/python/quikr.py index a756e6c..857cd25 100755 --- a/src/python/quikr.py +++ b/src/python/quikr.py @@ -57,6 +57,9 @@ 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 @@ -97,7 +100,11 @@ 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) |