erkiaun
commented
6 years ago The "PhenotypeSeeker prediction" was written according to gmer_caller version, which had header in the output file. However, the gmer_caller version in the bin folder gives output without header.
Fixed the "PhenotypeSeeker prediction" to work with either version of gmer_caller (the program that "PhenotypeSeeker prediction" uses to fast check the k-mers presence in samples).
Hi,
I created my own model for phenotype prediction with phenotypeseeker modeling (all with default parameters). If I now start the prediction with the output of the modelling (Did everything like it is described on the main page) I get following error:
File "/usr/local/bin/phenotypeseeker", line 213, in
Main()
File "/usr/local/bin/phenotypeseeker", line 207, in Main
args.func(args)
File "/usr/local/lib/python2.7/dist-packages/PhenotypeSeeker/prediction.py", line 147, in prediction
predict(samples_order, phenotypes_to_predict)
File "/usr/local/lib/python2.7/dist-packages/PhenotypeSeeker/prediction.py", line 117, in predict
predictions = model.predict(kmers_presence_matrix)
File "/usr/local/lib/python2.7/dist-packages/sklearn/utils/metaestimators.py", line 115, in
out = lambda *args, *kwargs: self.fn(obj, args, **kwargs)
File "/usr/local/lib/python2.7/dist-packages/sklearn/model_selection/_search.py", line 468, in predict
return self.bestestimator.predict(X)
File "/usr/local/lib/python2.7/dist-packages/sklearn/linear_model/base.py", line 324, in predict
scores = self.decision_function(X)
File "/usr/local/lib/python2.7/dist-packages/sklearn/linear_model/base.py", line 300, in decision_function
X = check_array(X, accept_sparse='csr')
File "/usr/local/lib/python2.7/dist-packages/sklearn/utils/validation.py", line 433, in check_array
array = np.array(array, dtype=dtype, order=order, copy=copy)
ValueError: setting an array element with a sequence.
Thanks for helping.