This repository, holds a collection of tools to readily work with FROG files.
The idea is to keep the library quite lightweight, so as to run with as few modules as possible.
probably best done in a virtual environment:
python3 -m venv venv
source ./venv/bin/activatethen either clone and install for editing:
git clone https://github.com/fbergmann/omex-frog.git
cd omex-frog
pip install -e . or directly from github:
pip install git+https://github.com/fbergmann/omex-frog.git>>> import omex_frog
>>> omex_frog.guess_format_uri('manifest.json')
'http://identifiers.org/combine.specifications:frog-json-version-1'Not much to this project yet, just a file for guessing format identifiers:
./venv/bin/guess_format ~/MODEL2211290003
would yield:
MODEL2211290003
---------------
MM_bound
--------
manifest.xml http://identifiers.org/combine.specifications:omex-manifest
FROG
----
cobrapy
-------
02_fva.tsv http://identifiers.org/combine.specifications:frog-fva-version-1
04_reaction_deletion 2.tsv http://identifiers.org/combine.specifications:frog-reactiondeletion-version-1
01_objective 2.tsv http://identifiers.org/combine.specifications:frog-objective-version-1
metadata 2.json http://identifiers.org/combine.specifications:frog-json-version-1
metadata.json http://identifiers.org/combine.specifications:frog-metadata-version-1
03_gene_deletion.tsv http://identifiers.org/combine.specifications:frog-genedeletion-version-1
frog.json http://identifiers.org/combine.specifications:frog-json-version-1
04_reaction_deletion.tsv http://identifiers.org/combine.specifications:frog-reactiondeletion-version-1
01_objective.tsv http://identifiers.org/combine.specifications:frog-objective-version-1
02_fva 2.tsv http://identifiers.org/combine.specifications:frog-fva-version-1
frog 2.json http://identifiers.org/combine.specifications:frog-json-version-1
cameo
-----
02_fva.tsv http://identifiers.org/combine.specifications:frog-fva-version-1
metadata.json http://identifiers.org/combine.specifications:frog-metadata-version-1
03_gene_deletion.tsv http://identifiers.org/combine.specifications:frog-genedeletion-version-1
frog.json http://identifiers.org/combine.specifications:frog-json-version-1
04_reaction_deletion.tsv http://identifiers.org/combine.specifications:frog-reactiondeletion-version-1
01_objective.tsv http://identifiers.org/combine.specifications:frog-objective-version-1
02_fva 2.tsv http://identifiers.org/combine.specifications:frog-fva-version-1
frog 2.json http://identifiers.org/combine.specifications:frog-json-version-1
iMMM22IC_bound_Condition15.xml http://identifiers.org/combine.specifications:sbml
MM_unbound.omex http://identifiers.org/combine.specifications:omex
MM_bound.omex http://identifiers.org/combine.specifications:omex
MM_unbound
----------
iMMM22IC_unbound.xml http://identifiers.org/combine.specifications:sbml
manifest.xml http://identifiers.org/combine.specifications:omex-manifest
FROG
----
cobrapy
-------
02_fva.tsv http://identifiers.org/combine.specifications:frog-fva-version-1
04_reaction_deletion 2.tsv http://identifiers.org/combine.specifications:frog-reactiondeletion-version-1
01_objective 2.tsv http://identifiers.org/combine.specifications:frog-objective-version-1
metadata 2.json http://identifiers.org/combine.specifications:frog-json-version-1
metadata.json http://identifiers.org/combine.specifications:frog-metadata-version-1
03_gene_deletion.tsv http://identifiers.org/combine.specifications:frog-genedeletion-version-1
frog.json http://identifiers.org/combine.specifications:frog-json-version-1
03_gene_deletion 2.tsv http://identifiers.org/combine.specifications:frog-genedeletion-version-1
04_reaction_deletion.tsv http://identifiers.org/combine.specifications:frog-reactiondeletion-version-1
01_objective.tsv http://identifiers.org/combine.specifications:frog-objective-version-1
02_fva 2.tsv http://identifiers.org/combine.specifications:frog-fva-version-1
frog 2.json http://identifiers.org/combine.specifications:frog-json-version-1
cameo
-----
02_fva.tsv http://identifiers.org/combine.specifications:frog-fva-version-1
metadata.json http://identifiers.org/combine.specifications:frog-metadata-version-1
03_gene_deletion.tsv http://identifiers.org/combine.specifications:frog-genedeletion-version-1
frog.json http://identifiers.org/combine.specifications:frog-json-version-1
03_gene_deletion 2.tsv http://identifiers.org/combine.specifications:frog-genedeletion-version-1
04_reaction_deletion.tsv http://identifiers.org/combine.specifications:frog-reactiondeletion-version-1
01_objective.tsv http://identifiers.org/combine.specifications:frog-objective-version-1