r00bit

numpy.core._exceptions.MemoryError

4

Hello, I have a large mgf file with the size of 25GB, and trying to calculate the similarity score between each pair of spectrum in the file. However, by calling...

Hi, Would please let me know the steps for running the deepnovo_main.py? I use the following command: _python deepnovo_main.py --search_denovo --train_dir plasma/testing_plasma.spectrum.mgf --denovo_feature plasma/testing_plasma.feature.csv_ I got the following error: ImportError:...

Getting nan score for spec2vec_similarity function

3

Hi, Using two similarity functions to compute similarity scores between spectra of two files: 1. Spec2vec: scores = calculate_scores(ref_spectrums, query_spectrums, spec2vec_similarity) 2. CosineGreedy: scores = calculate_scores(references=spectrums1, queries=spectrums2, similarity_function=CosineGreedy()) However, I've...

reduce the size score after calling calculate_stores

1

Hi, After training spec2vec model and creating spec2vec_similarity function, I used calculate_scores to find the similarity of spectra pairs scores = calculate_scores(reference_documents, query_spectrums, spec2vec_similarity) However the size scores is too...

ValueError

4

After running the following command: `python denovo.py --input example.mgf --model model.h5 --output example_prediction.tsv` I get this error lib/python3.7/site-packages/keras/engine/input_spec.py", line 200, in assert_input_compatibility raise ValueError(f'Layer "{layer_name}" expects {len(input_spec)} input(s),' V**alueError: Layer...