Skip to content
This repository was archived by the owner on Jun 17, 2024. It is now read-only.
This repository was archived by the owner on Jun 17, 2024. It is now read-only.

ValueError: 'R' is not in list #35

@tiramisutes

Description

@tiramisutes

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.

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions