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Mseditorapi #19

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c2fdd6b
polishing the code
Jul 2, 2022
dd83cec
mseditorapi polishing
Jul 23, 2022
dec44ec
mseditorapi polishing
Jul 23, 2022
d94cc14
final polish
Sep 15, 2022
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192 changes: 65 additions & 127 deletions modelseedpy/core/mseditorapi.py
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Original file line number Diff line number Diff line change
@@ -1,9 +1,10 @@
import logging
logger = logging.getLogger(__name__)
from cobra.core import Reaction
import cobra
import re

logger = logging.getLogger(__name__)

class MSEditorAPI:

@staticmethod
Expand All @@ -22,7 +23,7 @@ def remove_reactions(model, rxn_id_list = []):
# ASSUMPTIONS:
# an arrow will exist in the program, either =>, <=>, or <=
@staticmethod
def edit_reaction(model, rxn_id, direction=None, gpr=None, genome=None):
def edit_reaction(model, rxn_id, direction=None, gpr=None, genome=None): # !!! genome is never used
# Direction: =>, <=, or <=>
if direction is not None:
lower_bound = model.reactions.get_by_id(rxn_id).lower_bound
Expand Down Expand Up @@ -51,97 +52,80 @@ def edit_reaction(model, rxn_id, direction=None, gpr=None, genome=None):
if gpr is not None:
model.reactions.get_by_id(rxn_id).gene_reaction_rule = gpr
except:
raise Exception('invalid gpr statement, check parentheses') # not working, unsure exactly why
raise Exception(f'The gpr {gpr} is invalid. Perhaps check parentheses.') # not working, unsure exactly why

@staticmethod
def edit_biomass_compound(model,biomass_id,cpd_id,new_coef,rescale = 1):
def edit_biomass_compound(model, biomass_id, cpd_id, new_coef):
if cpd_id not in model.metabolites:
raise Exception('Metabolite', cpd_id, ' is not in the model.')
if biomass_id in model.reactions:
if cpd_id in model.metabolites:
model.reactions.get_by_id(biomass_id).add_metabolites({model.metabolites.get_by_id(cpd_id): new_coef},
combine=False)
else:
raise Exception('Metabolite', cpd_id, ' is not in the model.')
model.reactions.get_by_id(biomass_id).add_metabolites(
{model.metabolites.get_by_id(cpd_id): new_coef}, combine=False)
else: # if there is no biomass reaction
biomass_rxn = Reaction(biomass_id)
model.add_reaction(biomass_rxn)
if cpd_id in model.metabolites:
biomass_rxn.add_metabolites({model.metabolites.get_by_id(cpd_id): new_coef})
else:
raise Exception('Metabolite ', cpd_id, ' is not in the model.')
biomass_rxn.add_metabolites({model.metabolites.get_by_id(cpd_id): new_coef})

@staticmethod
def compute_molecular_weight(model, metabolite_id):
if metabolite_id not in model.metabolites:
raise Exception('Error, metabolite', metabolite_id, 'not found in the model')
raise ValueError(f'The metabolite {metabolite_id} is not defined in the model')
return model.metabolites.get_by_id(metabolite_id).formula_weight

@staticmethod

def add_custom_reaction(model,rxn_id,MSEquation,gpr = None,genome = None):
def add_custom_reaction(model, rxn_id, MSEquation, gpr=None, genome=None): # !!! genome is never used
new_rxn = Reaction(id=rxn_id)
# going on the assumption that all metabolites are present in the model
metabolites = {}
for key in MSEquation.equation:
met_id = key[0] + '_' + key[1]
for key, stoich in MSEquation.equation.items():
met_id = key[0]+'_'+key[1]
if met_id in model.metabolites:
metabolites[met_id] = MSEquation.equation[key]
metabolites[met_id] = stoich
else:
raise Exception("Error,", met_id, "not in model metabolites list")
raise ValueError(f"The {met_id} is not in model.")
model.add_reaction(new_rxn)
# new_rxn.gene_reaction_rule = gpr
new_rxn.add_metabolites(metabolites)
if gpr:
new_rxn.gene_reaction_rule = gpr

# adjust the bounds based on the arrow direction -1000, 1000, 0
if MSEquation.direction == 'left':
new_rxn.lower_bound = 0
new_rxn.upper_bound = 1000
if MSEquation.direction == '<':
new_rxn.lower_bound = -1000
new_rxn.upper_bound = 0
if MSEquation.direction == 'reversable':
elif MSEquation.direction == '=':
new_rxn.lower_bound = -1000
new_rxn.upper_bound = 1000

@staticmethod
def add_ms_reaction(model, rxn_id, modelseed, compartment_equivalents = {'0':'c0', '1':'e0'}, direction = 'forward'):#Andrew
def add_ms_reaction(model, rxn_id, modelseed, compartment_equivalents = {'0':'c0', '1':'e0'}, direction = '>'):#Andrew
''' Add a reaction with ModelSEED parameters to the FBA simulation
"model" (COBRA object): The metabolic model that is defined by COBRApy
"rxn_id" (Python object, string): The ModelSEED reaction id that will be added to the model
"Compartment_equivalents" (Python object, dictionary): The compartment codes that are used in formating the passed reactions
"direction" (Python object, string): The direction of the defined reaction
"modelseed" (ModelSEED object): The ModelSEED database that describes the reaction and metabolites of the argument
'''
modelseed_reaction = modelseed.get_seed_reaction(rxn_id)
reaction_stoich = modelseed_reaction.cstoichiometry
cobra_reaction = cobra.Reaction(rxn_id)
modelseed_reaction = modelseed.get_seed_reaction(rxn_id)
cobra_reaction.name = modelseed_reaction.data['name']
reaction_stoich = modelseed_reaction.cstoichiometry

metabolites_to_add = {}
for metabolite, stoich in reaction_stoich.items():
id = metabolite[0]
compound = modelseed.get_seed_compound(id).data
compartment_number = metabolite[1]
compartment_string = compartment_equivalents[compartment_number]

metabolites_to_add[cobra.Metabolite(id, name = compound['name'], compartment = compartment_string)] = stoich
metabolites_to_add[cobra.Metabolite(
metabolite[0], name = modelseed.get_seed_compound(metabolite[0]).data['name'],
compartment = compartment_equivalents[metabolite[1]])
] = stoich

cobra_reaction.add_metabolites(metabolites_to_add)
cobra_reaction.reaction

if direction == 'reversible':
cobra_reaction.lower_bound = 0
cobra_reaction.upper_bound = 1000
if direction == '=':
cobra_reaction.lower_bound = -1000
elif direction == 'backward':
elif direction == '<':
cobra_reaction.lower_bound = -1000
cobra_reaction.upper_bound = 0
elif direction == 'forward':
pass
else:
directions = ['forward', 'backward', 'reversible']
print('ERROR: The \'direction\' argument is not among the accepted {}, {}, and {} values.'.format(directions[0], directions[1], directions[2]))
direction = input('What is the direction of the reaction?')
while direction not in directions:
print('ERROR: The \'direction\' argument is not among the accepted {}, {}, and {} values.'.format(directions[0], directions[1], directions[2]))
direction = input('What is the direction of the reaction?')
MSEditorAPI.add_ms_reaction(model, rxn_id, modelseed, direction = direction)


model.add_reactions([cobra_reaction])

@staticmethod
Expand All @@ -150,113 +134,67 @@ def copy_model_reactions(model,source_model,rxn_id_list = []):
if rxnid in source_model.reactions:
model.add_reactions([source_model.reactions.get_by_id(rxnid)])
else:
raise Exception('The reaction', rxnid, 'in the reaction list is not in the model.')
raise ValueError(f'The {rxnid} reaction ID is not in the source model, and thus cannot be added to the model.')

@staticmethod
def copy_all_model_reactions(model,source_model): #new method that copies all reactions, may not be necessary
for rxn in source_model.reactions:
model.add_reactions([source_model.reactions.get_by_id(rxn.id)])

model.add_reactions([source_model.reactions.get_by_id(rxn.id) for rxn in source_model.reactions if rxn not in model.reactions])

class MSEquation:

def __init__(self, stoichiometry, d):
def __init__(self, stoichiometry, direction = None):
self.equation = stoichiometry
self.direction = d
self.direction = direction

@staticmethod
def build_from_palsson_string(equation_string, default_group='c'): # add default group

def clean_ends(lst):
"""
FIXME: use .strip
:param lst:
:return:
"""
for i in range(len(lst)):
# remove whitespace from the front
while lst[i][0] == ' ':
lst[i] = lst[i][1:]
# remove whitespace from the back
while lst[i][-1] == ' ':
lst[i] = lst[i][:-1]
return lst
return [i.strip() for i in lst]

def get_coef_and_group(lst, return_dict, side):
# for side variable, -1 is left side, 1 is right side, for coeficients
for reactant in lst:
for reagent in lst:
coeficient = side
if reactant.find('(') != -1 or reactant.find(
')') != -1: # if one is present, check to make sure both there
if equation_string.find(')') == -1:
raise Exception("Error, ')' character missing in string", reactant)
if equation_string.find('(') == -1:
raise Exception("Error, '(' character missing in string", reactant)
identifier = default_group
if '(' in reagent and ')' in reagent:
number = ''
position = 1
while reactant[position] != ')':
number += reactant[position]
while reagent[position] != ')':
number += reagent[position]
position += 1
coeficient = side * float(number)
reactant = reactant[position + 1:]

identifier = default_group
if reactant.find('[') != -1 or reactant.find(
']') != -1: # if one is present, check to make sure both there
# check to see both are present
if equation_string.find(']') == -1:
raise Exception("Error, ']' character missing in string", reactant)
if equation_string.find('[') == -1:
raise Exception("Error, '[' character missing in string", reactant)
reagent = reagent[position+1: ]
elif '[' in reagent and ']' in reagent:
s = ''
position = -2
while reactant[position] != '[':
s = reactant[position] + s
while reagent[position] != '[':
s = reagent[position] + s
position -= 1
identifier = s
reactant = reactant[:position]

return_dict[(reactant.strip(), identifier)] = coeficient
reagent = reagent[:position]
elif any([x in reagent for x in ['(', ')', '[', ']']]):
raise ValueError("A closing or opening parentheses or bracket is missing in the reaction string", reagent)
return_dict[(reagent.strip(), identifier)] = coeficient
return return_dict

# check for the '=' character, throw exception otherwise
if equation_string.find('=') == -1:
raise Exception("Error, '=' character missing, unable to split string", equation_string)

# check direction
reversible = False
right = False
left = False
ret_str = ''
reversible = equation_string.find('<=>') != -1
if reversible:
ret_str = '='
else: # not two ways, so check right
right = equation_string.find('=>') != -1
if right:
ret_str = '>'
else: # if not right, check left
left = equation_string.find('<=') != -1
if left:
ret_str = '<'
else: # if not left, error
ret_str = "?"
if '=' not in equation_string:
raise ValueError(f"Error: The '=' character is missing; hence, the reaction string {equation_string} cannot be split.")
if '<=>' in equation_string:
direction = '='
elif '=>' in equation_string:
direction = '>'
elif '<=' in equation_string:
direction = '<'
else:
direction = '?'

# cpd00001 + cpd00002[e] => (2)cpd00003 + cpd00004
# get substrings for either side of the euqation
# get substrings for either side of the equation
reactants_substring_list = equation_string[0:equation_string.find('=') - 1].split('+')
products_substring_list = equation_string[equation_string.find('=') + 2:len(equation_string)].split('+')

# clean up our substrings:
reactants_substring_list = list(map(lambda x: x.strip(), reactants_substring_list))
products_substring_list = list(map(lambda x: x.strip(), products_substring_list))

variables = {}
# add reactants to the dictionary

get_coef_and_group(reactants_substring_list, variables, -1)
get_coef_and_group(products_substring_list, variables, 1)

ret_mse = MSEquation(variables, ret_str)

return ret_mse
reactant_dict = get_coef_and_group([x.strip() for x in reactants_substring_list], {}, -1)
products_dict = get_coef_and_group([x.strip() for x in products_substring_list], reactant_dict, 1)
return MSEquation(reactant_dict.update(products_dict), direction)