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Switch blast execution from os to subprocess #63

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Switch blast execution from os to subprocess #63

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5 changes: 2 additions & 3 deletions kleborate/blastn.py
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Original file line number Diff line number Diff line change
Expand Up @@ -27,11 +27,10 @@ def run_blastn(db, query, min_cov, min_ident):
cmd += ' -dust no -evalue 1E-20 -word_size 32 -max_target_seqs 10000'
cmd += ' -perc_identity {}'.format(min_ident)

# TODO: switch this over to subprocess
blast_hits = []
f = os.popen(cmd)
f = subprocess.Popen(cmd, stdout=subprocess.PIPE, shell=True).stdout
for line in f:
blast_hits.append(BlastHit(line))
blast_hits.append(BlastHit(line.decode()))
f.close()

# Toss out low identity and low coverage hits.
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