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REF: import run_commands util from framework #176

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REF: import run_commands util from framework #176

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16 changes: 2 additions & 14 deletions q2_dada2/_denoise.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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