From 305daac154c75bde9985c19340eaebc0a026da17 Mon Sep 17 00:00:00 2001 From: valmikdesai Date: Thu, 23 Jul 2015 14:22:17 -0400 Subject: [PATCH] Min percent identity for Blast taxonomy assignment #243 Provided user an option to change minimum percent identity for Blast taxonomy assignment --- scripts/assign_taxonomy.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/scripts/assign_taxonomy.py b/scripts/assign_taxonomy.py index 6aeadf8442..fbd9142980 100755 --- a/scripts/assign_taxonomy.py +++ b/scripts/assign_taxonomy.py @@ -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: _assigned_taxonomy]') @@ -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