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cruizperez / MicrobeAnnotator

Pipeline for metabolic annotation of microbial genomes
Artistic License 2.0
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ko_mapper.py #60

Open mattoslmp opened 1 year ago

mattoslmp commented 1 year ago

Dear Dr. Carlos Ruiz. I intend use your script ko_mapper.py to generate kegg modules completenss (complete or not complete) using a ko list (Ex: ko_list.txt). I think that your script could give me this information. Can you provide a example of input format of ko_list.txt for ko_mapper.py ?

NataliHB commented 1 year ago

Hi,

I'd also appreciate and example of how to do format the input file.

fmauffrey commented 1 year ago

The input files are simply a list of KO numbers, with one KO per line.

K15523
K00254
K09765
K04750
K06978
K01318
...
javiercnav commented 3 months ago

Hello there, I have a tab file with the first column being a MAG-ID and second being a KO number. I am trying to run ko_mapper.py, and i got the following error: ./ko_mapper.py -i kos.genomes_copy.tsv --prefix output --cluster "both" Importing data... Traceback (most recent call last): File "./ko_mapper.py", line 623, in <module> main() File "./ko_mapper.py", line 615, in main module_information, metabolism_matrix, module_group_matrix = module_information_importer(input_files) File "./ko_mapper.py", line 93, in module_information_importer regular_modules = import_module_dict(data_folder / "01.KEGG_Regular_Module_Information.pickle") File "./ko_mapper.py", line 83, in import_module_dict pickle_in = open(dictionary_location,"rb") FileNotFoundError: [Errno 2] No such file or directory: 'data/01.KEGG_Regular_Module_Information.pickle' My guess is that I need to somehow indicate the location of my database. Am I correct? If so, how can I do this? Thanks a lot