mrqeoqqt / chemdistiller Goto Github PK

python RankTestJson.py C:\temp_out\annotated_spectra.json 0 C:\temp_out\ranking.txt
ranking.txt
python RankTestJson.py C:\temp_out\annotated_spectra.json 1 C:\temp_out\ranking.txt
ranking.txt

Each line output text is <No.>

Hi developer,

I was trying to run a test run using annotate.py, but all I got was an error message as the following:

Traceback (most recent call last):

  File "/Users/.../chemdistiller/annotate.py", line 597, in <module>
    run_annotation(args.input_spectra_folder, db_file, chemical_databases, args.output_folder, SVMs_path, ncpu, ppm, max_results_per_query, True);

  File "/Users/.../chemdistiller/annotate.py", line 333, in run_annotation
    for index in range(len(annotation.mol_candidates.mol_list)):

AttributeError: 'NoneType' object has no attribute 'mol_list'

Do you know what the problem is here and how to fix this?

Regards,
Katharine C

Fix a deprecated code

|D:\anaconda\envs\chemdistiller\lib\site-packages\h5py_init_.py:36: FutureWarning: Conversion of the second argument of issubdtype from float to np.floating is deprecated. In future, it will be treated as np.float64 == np.dtype(float).type.
from ._conv import register_converters as _register_converters

To start the program correctly, use
python annotate.py C:\temp\input C:\temp\output --ncpu 4 --delta_mz 20 --max_results 10

python MSP2ChemDistiller.py C:\MSP_data\MoNA-export-Fiehn_HILIC.msp 1 C:\MSP2Chem
input data:
MoNA-export-Fiehn_HILIC.txt
one output file sample:
4-Acetamidobutyric acid.txt
python MSP2ChemDistiller.py C:\MSP_data\FiehnLab-Exactive-460.txt 0 C:\MSP2Chem C:\Users\<user_name>\chemdistiller\Input_Sample\0_empty.txt
input data:
FiehnLab-Exactive-460.txt
one output file sample:
(2-oxo-2,3-dihydro-1H-indol-3-yl)acetic acid.txt