brsynth / brs-libs

Libraries for rpTools

brs-libs

Libraries for rpTools:

• rpSBML
• rpCache
• inchikeyMIRIAM

rpSBML

Defines SBML structure with additional fields relative to RetroPath2 objects.

rpCache

Memory management

File mode

This is the default mode. All cache data are stored into files on disk and loaded in memory each time the tool is used. In this mode, fingerprint in memory is equal to the size of cache files loaded in memory multiplied by the number of processes which are running at the same time. Option can be specified by --store-mode file.

DB mode

In order to save memory space, cache data can be loaded once in a database (redis) so that the memory space taken is equal to one instance of the cache, whatever the number of processes whic are running. Option can be specified by --store-mode <db_host>, where db_host is the hostname on which redis server is running.

Install

From Conda

[sudo] conda install -c brsynth -c conda-forge brs_libs

Use

Load rpCache in memory

Full cache into files

from brs_libs import rpCache

rpcache = rpCache(db='file')
print(rpcache.cid_src)

Full cache into Redis DB For multiple instances of rpCache simultaneously, rpCache can be loaded into one single Redis database:

from brs_libs import rpCache

rpcache = rpCache(db='localhost')
print(rpcache.cid_src)

localhost means that rpCache will look for a redis database locally. If there is not, it will start a brand new redis server. localhost could be replaced by any hostname that hosts the Redis database.

A part of cache For less loading time and memory footprint, a part of the cache can be loaded:

from brs_libs import rpCache

rpcache = rpCache(attrs='cid_strc')
print(rpcache.cid_src)

(Re-)generate the cache

From Python code

from brs_libs import rpCache

rpCache.generate_cache(outdir)

From CLI After having installed brs_libs Python module:

python -m brs_libs --gen_cache <folder>

Test

Please follow instructions below ti run tests:

cd tests
pytest -v

For further tests and development tools, a CI toolkit is provided in ci folder (see ci/README.md).

inchikeyMIRIAM

Uses the rpCache to parse an SBML file to find all the chemical species, and try to recover the inchikey and add it to the MIRIAM annotation.

Authors

• Melchior du Lac
• Joan Hérisson

Acknowledgments

• Thomas Duigou

Licence

brs_libs is released under the MIT licence. See the LICENCE file for details.