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ValueError: 'R' is not in list #35

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tiramisutes opened this issue Dec 27, 2020 · 0 comments
Open

ValueError: 'R' is not in list #35

tiramisutes opened this issue Dec 27, 2020 · 0 comments

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@tiramisutes
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Hi,
I always get the follows error when running Azimuth.

  File "/home/Azimuth-2.0/azimuth/model_comparison.py", line 559, in predict
    feature_sets = feat.featurize_data(Xdf, learn_options, pandas.DataFrame(), gene_position, pam_audit=pam_audit, length_audit=length_audit)
  File "/home/Azimuth-2.0/azimuth/features/featurization.py", line 31, in featurize_data
    get_all_order_nuc_features(data['30mer'], feature_sets, learn_options, learn_options["order"], max_index_to_use=30, quiet=quiet)
  File "/home/Azimuth-2.0/azimuth/features/featurization.py", line 153, in get_all_order_nuc_features
    include_pos_independent=True, max_index_to_use=max_index_to_use, prefix=prefix)
  File "/home/Azimuth-2.0/azimuth/features/featurization.py", line 423, in apply_nucleotide_features
    feat_pd = seq_data_frame.apply(nucleotide_features, args=(order, max_index_to_use, prefix, 'pos_dependent'))
  File "/home/lib/python2.7/site-packages/pandas/core/series.py", line 3194, in apply
    mapped = lib.map_infer(values, f, convert=convert_dtype)
  File "pandas/_libs/src/inference.pyx", line 1472, in pandas._libs.lib.map_infer
  File "/home/lib/python2.7/site-packages/pandas/core/series.py", line 3181, in <lambda>
    f = lambda x: func(x, *args, **kwds)
  File "/home/Azimuth-2.0/azimuth/features/featurization.py", line 468, in nucleotide_features
    features_pos_dependent[alphabet.index(nucl) + (position*len(alphabet))] = 1.0
ValueError: 'R' is not in list

Sometimes, also have the error ValueError: 'K' is not in list.
I have searched via Google, but no solution found.
So, how to solve the problemz? Thanks.

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