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Matteopaluh / KEMET

KEGG Module Evaluation Tool
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Custom Modules? #8

Closed michoug closed 1 year ago

michoug commented 2 years ago

Hi, I saw that the README indicated that custom modules could be added. Should they just be included in the kk_files folder, or do they need to be included elsewhere? Cheers Greg

Matteopaluh commented 2 years ago

Hi Greg, Yes, you're totally correct: custom modules should be included in the kk_files folder. Those files have a specific format that was generated via a script and a few modifications from the original KEGG MODULES entries.

Any user can include other modules by generating a file with ".kk" extension and the following format.

As an example, below are some indications as present in M00023.

M00023_Tryptophan biosynthesis, chorismate => tryptophan
K01657, K01658, K13503, K13501, K01656, K13497
K00766, K13497
K01817, K24017, K13498, K13501
K01656, K01609, K13498, K13501
K01695, K01696, K06001, K01694
COMPLEXES_LIST
K01657+K01658, K01695+K01696, K01695+K06001

1st line (indications that appear in the report files):

_ ### 2nd until end/extra lines: sequential KEGG orthologs alternatives for a single step, separated by a comma. ### Extra lines (in case of more complex reaction relations): - A "COMPLEXES_LIST" line enables multi-genes relations informations (e.g. K01657+K01658 for the first step of the exemplified module). - An "OPTIONAL_LIST" line includes KOs which are not mandatory for considering a module step complete, but KO presence/absence is still indicated in the report files. Thank you for your interest in KEMET! Cheers, Matteo EDIT: [here](https://github.com/Matteopaluh/KEMET/wiki/KEGG-Custom-Modules-analyses) for the wiki page listing all Module indications, derived from this issue answer.