psamm.importer – Import Functions

Entry points and functionality for importing models.

This module contains entry points for the psamm-import programs and functionality to assist in importing external file formats, converting them into proper native models and writing those models to files.

exception psamm.importer.ImportError

Exception used to signal a general import error.

exception psamm.importer.ModelLoadError

Exception used to signal an error loading the model files.

exception psamm.importer.ParseError

Exception used to signal an error parsing the model files.

class psamm.importer.Importer

Base importer class.

psamm.importer.get_default_compartment(model)

Return what the default compartment should be set to.

If some compounds have no compartment, unique compartment name is returned to avoid collisions.

psamm.importer.detect_best_flux_limit(model)

Detect the best default flux limit to use for model output.

The default flux limit does not change the model but selecting a good value reduced the amount of output produced and reduces clutter in the output files.

psamm.importer.reactions_to_files(model, dest, writer, split_subsystem)

Turn the reaction subsystems into their own files.

If a subsystem has a number of reactions over the threshold, it gets its own YAML file. All other reactions, those that don’t have a subsystem or are in a subsystem that falls below the threshold, get added to a common reaction file.

Parameters:
  • model – psamm_import.model.MetabolicModel.
  • dest – output path for model files.
  • writer – psamm.datasource.native.ModelWriter.
  • split_subsystem – Divide reactions into multiple files by subsystem.
psamm.importer.model_exchange(model)

Return exchange definition as YAML dict.

psamm.importer.model_reaction_limits(model)

Yield model reaction limits as YAML dicts.

psamm.importer.infer_compartment_entries(model)

Infer compartment entries for model based on reaction compounds.

psamm.importer.infer_compartment_adjacency(model)

Infer compartment adjacency for model based on reactions.

psamm.importer.count_genes(model)

Count the number of distinct genes in model reactions.

psamm.importer.write_yaml_model(model, dest='.', convert_exchange=True, split_subsystem=True)

Write the given NativeModel to YAML files in dest folder.

The parameter convert_exchange indicates whether the exchange reactions should be converted automatically to an exchange file.

psamm.importer.main(importer_class=None, args=None)

Entry point for import program.

If the args are provided, these should be a list of strings that will be used instead of sys.argv[1:]. This is mostly useful for testing.

psamm.importer.main_bigg(args=None, urlopen=<function urlopen>)

Entry point for BiGG import program.

If the args are provided, these should be a list of strings that will be used instead of sys.argv[1:]. This is mostly useful for testing.