fbergmann / omex-frog

OMEX Frog tools

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.

installing

probably best done in a virtual environment:

python3 -m venv venv
source ./venv/bin/activate

then 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

API

>>> import omex_frog
>>> omex_frog.guess_format_uri('manifest.json')
'http://identifiers.org/combine.specifications:frog-json-version-1'

Using

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