marsi package

Subpackages

• marsi.alembic package
  • Subpackages
    • marsi.alembic.versions package
      • Submodules
      • marsi.alembic.versions.c1b678211e9d_baseline module
      • marsi.alembic.versions.ef39a4ae2c8c_add_solubility module
      • Module contents
  • Submodules
  • marsi.alembic.env module
  • Module contents
• marsi.chemistry package
  • Submodules
  • marsi.chemistry.common module
  • marsi.chemistry.common_ext module
  • marsi.chemistry.molecule module
  • marsi.chemistry.openbabel module
  • marsi.chemistry.qsar module
  • marsi.chemistry.rdkit module
  • marsi.chemistry.solubility module
  • Module contents
• marsi.cli package
  • Subpackages
    • marsi.cli.controllers package
      • Submodules
      • marsi.cli.controllers.chemistry module
      • marsi.cli.controllers.database module
      • marsi.cli.controllers.modeling module
      • Module contents
  • Submodules
  • marsi.cli.app module
  • Module contents
• marsi.cobra package
  • Subpackages
    • marsi.cobra.flux_analysis package
      • Submodules
      • marsi.cobra.flux_analysis.analysis module
      • marsi.cobra.flux_analysis.manipulation module
      • Module contents
    • marsi.cobra.strain_design package
      • Submodules
      • marsi.cobra.strain_design.design_methods module
      • marsi.cobra.strain_design.evolutionary module
      • marsi.cobra.strain_design.metaheuristic module
      • marsi.cobra.strain_design.post_processing module
      • marsi.cobra.strain_design.target module
      • Module contents
  • Submodules
  • marsi.cobra.utils module
  • Module contents
• marsi.io package
  • Submodules
  • marsi.io.bigg module
  • marsi.io.build_database module
  • marsi.io.data module
  • marsi.io.db module
  • marsi.io.enrichment module
  • marsi.io.parsers module
  • marsi.io.plots module
  • marsi.io.retriaval module
  • Module contents
• marsi.nearest_neighbors package
  • Submodules
  • marsi.nearest_neighbors.model module
  • marsi.nearest_neighbors.model_ext module
  • Module contents

Submodules

marsi.bigg_api module

BiGG database API v2

class marsi.bigg_api.DBVersion(version, api_version, last_update)

Bases: object

Version container.

version

str – Database version.

api_version

str – Version of the API used.

last_update

str – Last update timestamp.

marsi.bigg_api.database_version()

Retrieves the current version of BiGG database

marsi.bigg_api.download_model(model_id, file_format='json', save=True, path='.')

Download models from BiGG. You can chose to save the file or to return the JSON data.

Parameters:

• model_id (str) – A valid id for a model in BiGG.
• file_format (str) –

  If you want to save the file, you can import the model in the following formats:

  1. json (JSON format)
  2. xml (SBML)
  3. xml.gz (SBML compressed)
  4. mat (MATLAB)

• save (bool) – If True, writes the model to a file with the model name (the path can be specified).
• path (str) – Specifies in which folder the model should be written if save is True.

marsi.bigg_api.model_details(model_id)

Summarize the model.

Parameters:model_id (str) – A valid id for a model in BiGG.

marsi.bigg_api.list_models()

Lists all models available in BiGG.

marsi.bigg_api.list_reactions()

List all reactions available in BiGG.

marsi.bigg_api.list_model_reactions(model_id)

List all reactions in a model.

Parameters:model_id (str) – A valid id for a model in BiGG.

marsi.bigg_api.get_reaction(reaction_id)

Retrieve a reaction from BiGG.

Parameters:reaction_id (str) – A valid id for a reaction in BiGG.

marsi.bigg_api.get_model_reaction(model_id, reaction_id)

Retrieve a reaction in the context of a model from BiGG.

Parameters:

• model_id (str) – A valid id for a model in BiGG.
• reaction_id (str) – A valid id for a reaction in BiGG.

marsi.bigg_api.list_metabolites()

List all metabolites in BiGG.

marsi.bigg_api.list_model_metabolites(model_id)

List all metabolites in a model.

Parameters:model_id (str) – A valid id for a model in BiGG.

marsi.bigg_api.get_metabolite(metabolite_id)

Retrieve a metabolite from BiGG.

Parameters:metabolite_id (str) – A valid id for a reaction in BiGG.

marsi.bigg_api.get_model_metabolite(model_id, metabolite_id)

Retrieve a metabolite in the context of a model from BiGG.

Parameters:

• metabolite_id (str) – A valid id for a reaction in BiGG.
• model_id (str) – A valid id for a model in BiGG.

marsi.bigg_api.list_model_genes(model_id)

List all genes in a model.

Parameters:model_id (str) – A valid id for a model in BiGG.

marsi.bigg_api.get_model_gene(model_id, gene_id)

Retrieve a gene in the context of a model from BiGG.

Parameters:

• model_id (str) – A valid id for a model in BiGG.
• gene_id (str) – A valid id for a gene in BiGG.

marsi.bigg_api.search(query, search_type)

Fuzzy search the BiGG database.

Parameters:

• query (str) – Whatever you are searching for (ids, names, etc…).
• search_type (str) – Search domain. One of “models”, “genes”, “reactions”, “metabolites”.

marsi.config module

class marsi.config.Level

Bases: object

ERROR = 0

WARNING = 1

INFO = 2

DEBUG = 4

marsi.utils module

marsi.utils.pickle_large(obj, file_path, progress=False)

marsi.utils.unpickle_large(file_path, progress=False)

marsi.utils.frange(start, stop=None, steps=10)

Float range generator.

Generates steps equally separated between start and stop. If stop is None, the values are between 0 and start

Parameters:

• start (float) – The initial value.
• stop (float) – The final value.
• steps (int) – Number of values to generate.

Returns:

A generator that yields float.

Return type:

generator

Module contents