marsi.cli.controllers package

Submodules

marsi.cli.controllers.chemistry module

class marsi.cli.controllers.chemistry.ChemistryController(*args, **kw)

Bases: cement.core.controller.CementBaseController

This is the Optimization Controller. It allows to run optimizations from the command line.

Methods

Meta
default()
find_analogs()	Make a fingerprint from the –inchi, –sdf or –mol.

class Meta

Bases: object

label = 'chem'

stacked_on = 'base'

stacked_type = 'nested'

description = 'Metabolite database query and filter tools'

arguments = [(['--inchi'], {'help': 'The metabolite InChI to search'}), (['--sdf'], {'help': 'The metabolite SDF to search'}), (['--mol'], {'help': 'The metabolite MOL to search'}), (['--fingerprint-format', '-fp'], {'default': 'maccs', 'help': 'The fingerprint format', 'action': 'store'}), (['--fingerprint-cutoff', '-fpcut'], {'default': 'dynamic', 'help': 'Fingerprint cutoff', 'action': 'store'}), (['--similarity-cutoff', '-scut'], {'default': None, 'help': 'Similarity cutoff', 'action': 'store'}), (['--neighbors', '-k'], {'help': 'Filter the first K hits'}), (['--radius', '-r'], {'help': 'Filter hits within R distance radius'}), (['--atoms-weight', '-aw'], {'help': 'The weight of the atoms for structural similarity'}), (['--bonds-weight', '-bw'], {'help': 'The weight of the bonds for structural similarity'}), (['--atoms-diff', '-ad'], {'help': 'The maximum number of the atoms difference for database query'}), (['--bonds-diff', '-bd'], {'help': 'The maximum number of the bonds difference for database query'}), (['--rings-diff', '-rd'], {'help': 'The maximum number of the rings difference for database query'}), (['--output-file', '-o'], {'help': 'Output file'}), (['--output-format', '-f'], {'default': 'csv', 'help': 'Output format (default: csv)'})]

default()

find_analogs()

1. Make a fingerprint from the –inchi, –sdf or –mol.
2. Query the database

marsi.cli.controllers.database module

class marsi.cli.controllers.database.DatabaseController(*args, **kw)

Bases: cement.core.controller.CementBaseController

Methods

Meta
add_known_analogs()
build_data()
build_database()
default()
download()
download_bigg()
download_chebi()
download_drug_bank()
download_kegg()
download_pubchem()
download_zinc()
init()
migrate()	Run database migration.
status()

class Meta

Bases: object

label = 'db'

stacked_on = 'base'

stacked_type = 'nested'

description = 'Initialise MARSI (download data and build initial database)'

arguments = [(['--drugbank-version'], {'help': 'DrugBank version (5.0.3)'}), (['--with-zinc'], {'action': 'store_true', 'help': 'Include Zinc'})]

default()

init()

migrate()

Run database migration.

download()

download_chebi()

download_drug_bank()

download_bigg()

download_pubchem()

download_zinc()

download_kegg()

status()

build_data()

build_database()

add_known_analogs()

marsi.cli.controllers.modeling module

class marsi.cli.controllers.modeling.OptimizationController(*args, **kw)

Bases: cement.core.controller.CementBaseController

This is the Optimization Controller. It allows to run optimizations from the command line.

Methods

Meta
ale()	Load model specified by –model.
convert()	Load model specified by –model.
default()
mutagenesis()	Load model specified by –model.

exclude_reactions = ['ATPM']

class Meta

Bases: object

label = 'optimize'

stacked_on = 'base'

stacked_type = 'nested'

description = 'Optimize a host phenotype using Metabolites as targets'

arguments = [(['--model', '-m'], {'help': 'path or identifier of the model to be used'}), (['--carbon-source'], {'help': '(optional) the carbon source exchange reaction. It will be auto-detected if not defined'}), (['--target', '-t'], {'help': 'The exchange reaction of the target phenotype or the metabolite to accumulate'}), (['--approach', '-a'], {'help': 'classic: use reaction search; metabolites: search for metabolite targets directly. (default: classic)'}), (['--biomass'], {'help': '(optional) the biomass reaction (needed if there is none or many reactions containing biomass on their ids or names'}), (['--max-interventions', '-mi'], {'help': '(optional) maximum number of interventions (default: 2)'}), (['--max-evaluations', '-me'], {'help': '(optional) maximum number of evaluations (default: 20000)'}), (['--output-file', '-o'], {'help': 'output file'}), (['--input-file', '-i'], {'help': 'input file'}), (['--transporters'], {'help': 'Include transporters knockout'})]

default()

mutagenesis()

1. Load model specified by –model.
2. Detect carbon source if not defined, otherwise change the carbon source.
3. Detect biomass if not defined
4. Run the optimization.
5. Return the results.

ale()

1. Load model specified by –model.
2. Detect carbon source if not defined, otherwise change the carbon source.
3. Detect biomass if not defined
4. Run the optimization.
5. Return the results.

convert()

1. Load model specified by –model.
2. Detect carbon source if not defined, otherwise change the carbon source.
3. Detect biomass if not defined
4. Convert the results.

Module contents

class marsi.cli.controllers.MarsiBaseController(*args, **kw)

Bases: cement.core.controller.CementBaseController

This is the application base controller.

Methods

Meta
db_status()
default()	Download necessary files.

class Meta

Bases: object

label = 'base'

default()

1. Download necessary files.
2. Build the data files.
3. Build the database.

db_status()