https://github.com/cfrioux/padmet-tricks
Some tiny scripts involving padmet to hack metabolic networks
https://github.com/cfrioux/padmet-tricks
Last synced: 7 months ago
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Some tiny scripts involving padmet to hack metabolic networks
- Host: GitHub
- URL: https://github.com/cfrioux/padmet-tricks
- Owner: cfrioux
- Created: 2020-05-25T11:46:38.000Z (about 6 years ago)
- Default Branch: master
- Last Pushed: 2023-11-29T17:29:31.000Z (over 2 years ago)
- Last Synced: 2025-09-10T00:18:37.230Z (9 months ago)
- Language: Python
- Size: 14.6 KB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# padmet-tricks
Some tiny scripts involving padmet to hack metabolic networks
## Creation of a sbml with desired set of reactions only
`subnetwork.py`
Inputs:
* an empty padmet `data/empty.padmet`
* a list of reactions
* a padmet file with the reactions data
* an output SBML file
* option to remove cofactors (defined in the script) from the reactions
```shell
python subnetwork.py --help
```
## Creation of a sbml with desired set of pathways only
`extract_pathways.py`
Inputs:
* an empty padmet `data/empty.padmet`
* a pathway name
* a padmet file with the reactions data
* an output SBML file
```shell
python extract_pathways.py --help
```
## Analyse the ontology of compounds and pathways in metacyc
`cpd_ontology.py` and `pwy_ontology.py`
build a tree with all parent/children relationships used to describe metabolites and metabolic pathways in Metacyc.
`get_high_lvl_cpds.py` and `get_high_lvl_pwys.py` use the previous ontology (nw file) to get the high level parents of a list of compounds/pathways.
`padmet_cpd_to_highlevel_onto.py` and `padmet_pwys_to_highlevel_onto.py` use the previous ontology (nw file) to get the high level parents of all compounds/pathways from a padmet file.
`get_family_metabolites.py` retrieves the families of given compounds and pathways using families ontology (json file).
`analyse_all_mn_cpds.py` and `analyse_all_mn_pwys.py` analyse the pathways or metabolites of directory of metabolic networks and retrieve for each of them the representation of each category of compounds/pathway using a json ontology of Metacyc.
`onto_json_to_long_format` create tabulated files out of the json ontologies of pathways.