how to generate psm header file and errors occur with graph construction

[irleader]

In graph construction, <psm header name without 'csv'>, how to generate a psm header file from any original .mgf file?

When I do graph construction with the supplied "A_Thaliana.csv" and "A_Thaliana.mgf" under the same folder, there is error:

File "D:\GraphNovo\genova\utils\graph_constructor.py", line 332, in product_ion_info = all_spectra[spec_index] KeyError: 'A_Thaliana:F2.2:97749'

When I do graph construction with the supplied "C_Elegans.csv" and "C_Elegans.mgf" as well as "E_Coli.csv" and "E_Coli.mgf", there is another error:

Traceback (most recent call last): File "D:\GraphNovo\genova\utils\graph_constructor.py", line 335, in node_mass, node_input, rel_input, edge_input, graph_label = graph_gen(seq, product_ions_moverz, product_ions_intensity, precursor_ion_mass, precursor_charge>2) File "D:\GraphNovo\genova\utils\graph_constructor.py", line 152, in call subedge_maxnum, edge_type, edge_error = self.edge_generator(node_mass,precursor_ion_mass) File "D:\GraphNovo\genova\utils\graph_constructor.py", line 271, in edge_generator edge_type, edge_error = edge_matrix_generator(n, File "edge_matrix_gen.pyx", line 13, in edge_matrix_gen.edge_matrix_generator long[:,::1] start_edge_type, ValueError: Buffer dtype mismatch, expected 'long' but got 'long long'

[SamvPy]

Hi,

Were you able to fix this already? I am lost how the required psm header file should be generated from an MGF.

Thanks in advance!

-Sam

[codjjj]

Hi, I'm also wandering how I can convert the initial (csv,mgf) file to construct the graph ? README said cd genova/utils sh parrllel_preprocessing.sh <total_threads> <data_path> <psm header name without 'csv'> but where is the parrllel_preprocessing.sh? Thansk in advance!