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Min percent identity for Blast taxonomy assignment #2063

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Min percent identity for Blast taxonomy assignment #2063

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4 changes: 4 additions & 0 deletions scripts/assign_taxonomy.py
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Original file line number Diff line number Diff line change
Expand Up @@ -211,6 +211,9 @@
make_option('-e', '--blast_e_value', type='float',
help='Maximum e-value to record an assignment, only used for blast '
'method [default: %default]', default=0.001),
make_option('--identity', type='float',
help='Minimum percent identity to record an assignment, only used for blast '
'method [default: %default]',default=90.0),
make_option('-o', '--output_dir', type='new_dirpath',
help='Path to store result file ' +
'[default: <ASSIGNMENT_METHOD>_assigned_taxonomy]')
Expand Down Expand Up @@ -334,6 +337,7 @@ def main():
else:
params['reference_seqs_filepath'] = opts.reference_seqs_fp
params['Max E value'] = opts.blast_e_value
params['Min percent identity'] = opts.identity

elif assignment_method == 'mothur':
params['Confidence'] = opts.confidence
Expand Down