escher_maps_utils

Attributes

`BIGG_COFACTORS`
`BIGG_BUILDING_BLOCLS`
`MODELSEED_COFACTORS`
`EXCLUDED_COMPOUNDS`

Functions

`remove_cycles`(hierarchy)	Takes a {parent: (child,…)} hierarchy and returns the same structure
`build_reaction_hierarchy`(reaction_dict)
`build_escher_map`(model[, type, reaction_list, ...])	Build Escher map from cobra model.

Module Contents

escher_maps_utils.BIGG_COFACTORS = ['atp_c0', 'atp_c', 'adp_c', 'adp_c0', 'atp_c0', 'atp_c', 'adp_c', 'adp_c0', 'udp_c0', 'udp_c',...

escher_maps_utils.BIGG_BUILDING_BLOCLS = ['ala_L_c0', 'asp_L_c0', ' gln_L_c0', 'glu_L_c0', 'glu_L_c0', 'ser_L_c0', 'trp_L_c0',...

escher_maps_utils.MODELSEED_COFACTORS = ['cpd00001_c0', 'cpd00002_c0', 'cpd00003_c0', 'cpd00004_c0', 'cpd00005_c0', 'cpd00006_c0',...

escher_maps_utils.EXCLUDED_COMPOUNDS

escher_maps_utils.remove_cycles(hierarchy): Takes a {parent: (child,…)} hierarchy and returns the same structure with cycles removed (based on DFS). All original keys are preserved, even if they end up with no children.

escher_maps_utils.build_reaction_hierarchy(reaction_dict)

escher_maps_utils.build_escher_map(model, type: Literal['pathway', 'graph'] = 'pathway', reaction_list=[], pathway=None, KEGG_pathway_id=None, map_name='test_map', vertical=False, prev_gc={})

Build Escher map from cobra model.

Example:: glycolysis = [‘ALCD2x’, ‘ENO’, ‘FBA’, ‘FBP’, ‘GAPD’, ‘PFK’, ‘PGK’, ‘PGM’, ‘PPCK’, ‘PPS’, ‘PYK’, ‘TPI’] ppp = [‘FBA’, ‘FBP’, ‘GND’, ‘PFK’, ‘PGL’, ‘RPE’, ‘RPI’, ‘TKT1’]