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Summary fixes #76

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merged 2 commits into from
May 5, 2016
Merged

Summary fixes #76

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a28f70e
filter by default
martinghunt May 5, 2016
f628a22
has_res should be yes or no, never NA
martinghunt May 5, 2016
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2 changes: 1 addition & 1 deletion ariba/summary.py
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Original file line number Diff line number Diff line change
Expand Up @@ -119,7 +119,7 @@ def _gather_output_rows(self):
else:
rows[filename][cluster] = {
'assembled': 'no',
'has_res': 'NA',
'has_res': 'no',
'ref_seq': 'NA',
'known_var': 'NA',
'novel_var': 'NA',
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4 changes: 2 additions & 2 deletions ariba/tasks/summary.py
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Expand Up @@ -71,8 +71,8 @@ def run():
parser.add_argument('--cluster_cols', help='Comma separated list of cluster columns to include. Choose from: assembled, has_res, ref_seq, pct_id, known_var, novel_var [%(default)s]', default='has_res', metavar='col1,col2,...')
parser.add_argument('--col_filter', choices=['y', 'n'], default='y', help='Choose whether columns where all values are "no" or "NA" are removed [%(default)s]', metavar='y|n')
parser.add_argument('--row_filter', choices=['y', 'n'], default='y', help='Choose whether rows where all values are "no" or "NA" are removed [%(default)s]', metavar='y|n')
parser.add_argument('--known_vars', choices=['y', 'n'], default='y', help='Output a column for every known variant [%(default)s]', metavar='y|n')
parser.add_argument('--novel_vars', choices=['y', 'n'], default='y', help='Output a column for every novel variant [%(default)s]', metavar='y|n')
parser.add_argument('--known_vars', choices=['y', 'n'], default='n', help='Output a column for every known variant [%(default)s]', metavar='y|n')
parser.add_argument('--novel_vars', choices=['y', 'n'], default='n', help='Output a column for every novel variant [%(default)s]', metavar='y|n')
parser.add_argument('--min_id', type=float, help='Minimum percent identity cutoff to count as assembled [%(default)s]', default=90, metavar='FLOAT')
parser.add_argument('--verbose', action='store_true', help='Be verbose')
parser.add_argument('outprefix', help='Prefix of output files')
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4 changes: 2 additions & 2 deletions ariba/tests/summary_test.py
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Expand Up @@ -109,7 +109,7 @@ def test_gather_output_rows(self):
},
'variants_only1': {
'assembled': 'no',
'has_res': 'NA',
'has_res': 'no',
'ref_seq': 'NA',
'known_var': 'NA',
'novel_var': 'NA',
Expand All @@ -135,7 +135,7 @@ def test_gather_output_rows(self):
},
'variants_only1': {
'assembled': 'no',
'has_res': 'NA',
'has_res': 'no',
'ref_seq': 'NA',
'known_var': 'NA',
'novel_var': 'NA',
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