I ran into an error running on exome data. in the preprocess_sample.py
Traceback (most recent call last):
File "/fslustre/qhs/ext_sicotte_hugues_mayo_edu/projects/sinha/ecole_cnv/ECOLE-0.2/scripts/preprocess_sample.py", line 101, in
labeled_data = np.asarray(labeled_data)
ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 2 dimensions. The detected shape was (184526, 5) + inhomogeneo
us part.
The issue is of a variable length string as the sample name.
The fix was to change the last few lines.. in Bold are the code changes.
The “next” script in the pipeline works after that change too.
labeled_data = np.asarray(labeled_data, dtype=object) # FIXED
np.save(
os.path.join(output_path, sample_name + "_labeled_data.npy"),
labeled_data,
allow_pickle=True # FIXED
)
I ran into an error running on exome data. in the preprocess_sample.py
Traceback (most recent call last):
File "/fslustre/qhs/ext_sicotte_hugues_mayo_edu/projects/sinha/ecole_cnv/ECOLE-0.2/scripts/preprocess_sample.py", line 101, in
labeled_data = np.asarray(labeled_data)
ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 2 dimensions. The detected shape was (184526, 5) + inhomogeneo
us part.
The issue is of a variable length string as the sample name.
The fix was to change the last few lines.. in Bold are the code changes.
The “next” script in the pipeline works after that change too.
labeled_data = np.asarray(labeled_data, dtype=object) # FIXED
np.save(
os.path.join(output_path, sample_name + "_labeled_data.npy"),
labeled_data,
allow_pickle=True # FIXED
)