minedatabase 1.0.0

Metabolic In silico Network Expansions

MINE Databases

This repository contains code for the generation (though Pickaxe), storage and querying of MINE databases. For generalinformation on MINE Databases, please consult JJeffryes et al. 2015 APIs can found in the API Repository

Repository Structure

This repository primarily consists of the minedatabases python module and it's 5 submodules:

• compound_io: Contains functions to load and export chemical structures from MINE databases. Has command-line interface.
• databases: Contains functions which impose a schema on the underlying Mongo databases which store MINE data.
• pickaxe: Allows for the application of reaction rules to compound sets and the annotation of the resulting compounds an reactions. Has command-line interface.
• queries: Contains logic for text and chemical structure queries of the MINE database.
• utils: Various utility functions such as hashing & type conversions

Compound_io command-line usage

compound_io may be called independently to import or export chemical strictures in MINE database format. These may be helpful for sharing predictions or maintaining current external databases for cross-referencing. The call format is python compound_io.py import-<format> <input path> <database> for imports and python compound_io.py export-<format> <database> <outfile path> <optionally: maximum compounds per file> for exports. Valid formats are:

• smi: SMILES line-code
• mol: MDL molecule files (outputs individual files in specified directory)
• sdf: Structured Data File (concatenated mol files)
• tsv: FOR EXPORT ONLY, a tab separated file compatible with ModelSEED

Pickaxe command-line usage

Pickaxe.py can be called independently to generate predictions with or without database storage. To list all options call python pickaxe.py -h. To predict all chemical damage reactions for one generation on compounds in the iAF1260 model one would call python pickaxe.py -C ./data/ChemicalDamageCoreactants.tsv -r ./data/ChemicalDamageRxnRules.tsv -g 1 -c ./data/iAF1260.tsv

Testing

pytest to run all tests. Ensure that pytest is installed. To add coverage, run: pytest --cov-report term --cov-report xml:tests/cov.xml --cov=minedatabase minedatabase/tests/ Ensure that coverage and pytest-cov are both installed.