https://github.com/cfrioux/padmet-tricks

Some tiny scripts involving padmet to hack metabolic networks
https://github.com/cfrioux/padmet-tricks

Last synced: about 1 month 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 (over 4 years ago)
• Default Branch: master
• Last Pushed: 2023-11-29T17:29:31.000Z (about 1 year ago)
• Last Synced: 2023-12-11T12:30:18.022Z (about 1 year ago)
• Language: Python
• Size: 14.6 KB
• Stars: 0
• Watchers: 1
• 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.