diff --git a/q2_dada2/_denoise.py b/q2_dada2/_denoise.py index 081bc70..0a1bcc3 100644 --- a/q2_dada2/_denoise.py +++ b/q2_dada2/_denoise.py @@ -18,26 +18,14 @@ import pandas as pd import numpy as np +from qiime2.sdk.util import run_commands + from q2_types.feature_data import DNAIterator from q2_types.per_sample_sequences import ( SingleLanePerSampleSingleEndFastqDirFmt, SingleLanePerSamplePairedEndFastqDirFmt) -def run_commands(cmds, verbose=True): - if verbose: - print("Running external command line application(s). This may print " - "messages to stdout and/or stderr.") - print("The command(s) being run are below. These commands cannot " - "be manually re-run as they will depend on temporary files that " - "no longer exist.") - for cmd in cmds: - if verbose: - print("\nCommand:", end=' ') - print(" ".join(cmd), end='\n\n') - subprocess.run(cmd, check=True) - - def _check_featureless_table(fp): with open(fp) as fh: # There is a comment line and a header before the feature data