lobolab / mergem Goto Github PK

import mergem
from mergem import translate, load_model, save_model, map_localization, map_metabolite_univ_id, map_reaction_univ_id, get_metabolite_properties, get_reaction_properties, update_id_mapper
   
translated_model = mergem.translate(model, 'bigg')

import mergem
from mergem import translate, load_model, save_model, map_localization, map_metabolite_univ_id, map_reaction_univ_id, get_metabolite_properties, get_reaction_properties, update_id_mapper
    
translated_model = mergem.translate(model, trans_to_db='bigg')

(cobrapy_env) nfarooqi@M4819 gsm % mergem lhelveticus.sbml -t bigg
mergem, v0.26.2
Model does not contain SBML fbc package information.
SBML package 'layout' not supported by cobrapy, information is not parsed
SBML package 'render' not supported by cobrapy, information is not parsed
Use of the species charge attribute is discouraged, use fbc:charge instead: <Species M_cpd00443_c0 "ABEE_c0">
Use of the species charge attribute is discouraged, use fbc:charge instead: <Species M_cpd02920_c0 "2_Amino_4_hydroxy_6_hydroxymethyl_7_8_dihydropteridinediphosphate_c0">
Use of the species charge attribute is discouraged, use fbc:charge instead: <Species M_cpd00012_c0 "PPi_c0">
Use of the species charge attribute is discouraged, use fbc:charge instead: <Species M_cpd00067_c0 "H_plus__c0">
Use of the species charge attribute is discouraged, use fbc:charge instead: <Species M_cpd00683_c0 "Dihydropteroate_c0">
Use of the species charge attribute is discouraged, use fbc:charge instead: <Species M_cpd00114_c0 "IMP_c0">
Use of the species charge attribute is discouraged, use fbc:charge instead: <Species M_cpd00103_c0 "PRPP_c0">
Use of the species charge attribute is discouraged, use fbc:charge instead: <Species M_cpd00226_c0 "HYXN_c0">
Use of the species charge attribute is discouraged, use fbc:charge instead: <Species M_cpd00001_c0 "H2O_c0">
Use of the species charge attribute is discouraged, use fbc:charge instead: <Species M_cpd01759_c0 "N_Acyl_L_aspartate_c0">
Use of the species charge attribute is discouraged, use fbc:charge instead: <Species M_cpd00041_c0 "L_Aspartate_c0">
Use of the species charge attribute is discouraged, use fbc:charge instead: <Species M_cpd00049_c0 "Carboxylic_acid_c0">
Use of the species charge attribute is discouraged, use fbc:charge instead: <Species M_cpd00002_c0 "ATP_c0">
Use of the species charge attribute is discouraged, use fbc:charge instead: <Species M_cpd00008_c0 "ADP_c0">
Use of the species charge attribute is discouraged, use fbc:charge instead: <Species M_cpd00009_c0 "Phosphate_c0">
Use of the species charge attribute is discouraged, use fbc:charge instead: <Species M_cpd00947_c0 "LacCer_c0">
Use of the species charge attribute is discouraged, use fbc:charge instead: <Species M_cpd00108_c0 "Galactose_c0">
Use of the species charge attribute is discouraged, use fbc:charge instead: <Species M_cpd00878_c0 "Glucocerebroside_c0">
Use of the species charge attribute is discouraged, use fbc:charge instead: <Species M_cpd00022_c0 "Acetyl_CoA_c0">
cont....