6.1.1.3.1.3. pytfa.io.enrichment

Tools to import or export enrichment to and from pytfa models

6.1.1.3.1.3.1. Module Contents

6.1.1.3.1.3.1.1. Functions

write_lexicon(tmodel, filepath)

Writes a csv file in the format :

annotate_from_lexicon(model, lexicon)

Converts a lexicon into annotation for the metabolites

read_lexicon(filepath)

write_compartment_data(tmodel, filepath)

param filepath

read_compartment_data(filepath)

apply_compartment_data(tmodel, compartment_data)

pytfa.write_lexicon(tmodel, filepath)
Writes a csv file in the format :

seed_id

13BDglcn_c cpd11791 13dpg_c cpd00203 2pg_c cpd00482 3pg_c cpd00169 4abut_c cpd00281

Useful for exporting an annotation

Parameters
  • tmodel (pytfa.core.ThermoModel) –

  • filepath

Returns

pytfa.annotate_from_lexicon(model, lexicon)

Converts a lexicon into annotation for the metabolites

Parameters
  • model (cobra.Model) –

  • lexicon

Returns

pytfa.read_lexicon(filepath)
pytfa.write_compartment_data(tmodel, filepath)
Parameters
  • filepath

  • tmodel (pytfa.core.ThermoModel) –

Returns

pytfa.read_compartment_data(filepath)
pytfa.apply_compartment_data(tmodel, compartment_data)