IO
plaintext contains the functions to read and write stoichiometric models in plaintext. stoic contains a function to generate a list of reaction strings, ready to be written in plaintext, given a stoichiometric matrix.
Plaintext
This module implements methods for reading and writing models using a plain text format. Adapted from https://github.com/cdanielmachado/framed
Author: Daniel Machado
- set_up_grasp_models.io.plaintext.import_model_from_plaintext(filename)
Reads a model from a file.
- Parameters
filename (
str) – file path.- Return type
- Returns
A Model object (or respective subclass).
- set_up_grasp_models.io.plaintext.write_to_plaintext(rxn_strings, file_out, print_instructions=True)
Writes a model to a file.
- Parameters
rxn_strings (
list) – list of string reactions.file_out (
str) – file path.print_instructions (
bool) – print plain text format instructions as header.
- Returns
None
Stoic
- set_up_grasp_models.io.stoic.import_stoic(file_in)
Gets the reaction strings from the stoichiometry matrix defined in the GRASP input models.
- Parameters
file_in (
str) – path to file containing the model.- Return type
tuple- Returns
A metabolite list, a reaction list, and a reaction strings list.