def save_yaml_model(model, filename, sort=False, **kwargs):
"""
Write the cobra model to a file in YAML format.
``kwargs`` are passed on to ``yaml.dump``.
Parameters
----------
model : cobra.Model
The cobra model to represent.
filename : str or file-like
File path or descriptor that the YAML representation should be
written to.
sort : bool, optional
Whether to sort the metabolites, reactions, and genes or maintain the
order defined in the model.
See Also
--------
to_yaml : Return a string representation.
ruamel.yaml.dump : Base function.
"""
obj = model_to_dict(model, sort=sort)
obj["version"] = YAML_SPEC
if isinstance(filename, string_types):
with io.open(filename, "w") as file_handle:
yaml.dump(obj, file_handle, **kwargs)
else:
yaml.dump(obj, filename, **kwargs)
def save_yaml_model(model, filename, sort=False, **kwargs):
"""
Write the cobra model to a file in YAML format.
``kwargs`` are passed on to ``yaml.dump``.
Parameters
----------
model : cobra.Model
The cobra model to represent.
filename : str or file-like
File path or descriptor that the YAML representation should be
written to.
sort : bool, optional
Whether to sort the metabolites, reactions, and genes or maintain the
order defined in the model.
See Also
--------
to_yaml : Return a string representation.
ruamel.yaml.dump : Base function.
"""
obj = model_to_dict(model, sort=sort)
obj["version"] = YAML_SPEC
if isinstance(filename, string_types):
with io.open(filename, "w") as file_handle:
yaml.dump(obj, file_handle, **kwargs)
else:
yaml.dump(obj, filename, **kwargs)
def to_yaml(model, sort=False, **kwargs):
"""
Return the model as a YAML document.
``kwargs`` are passed on to ``yaml.dump``.
Parameters
----------
model : cobra.Model
The cobra model to represent.
sort : bool, optional
Whether to sort the metabolites, reactions, and genes or maintain the
order defined in the model.
Returns
-------
str
String representation of the cobra model as a YAML document.
See Also
--------
save_yaml_model : Write directly to a file.
ruamel.yaml.dump : Base function.
"""
obj = model_to_dict(model, sort=sort)
obj["version"] = YAML_SPEC
return yaml.dump(obj, **kwargs)
def to_json(model, sort=False, **kwargs):
"""
Return the model as a JSON document.
``kwargs`` are passed on to ``json.dumps``.
Parameters
----------
model : cobra.Model
The cobra model to represent.
sort : bool, optional
Whether to sort the metabolites, reactions, and genes or maintain the
order defined in the model.
Returns
-------
str
String representation of the cobra model as a JSON document.
See Also
--------
save_json_model : Write directly to a file.
json.dumps : Base function.
"""
obj = model_to_dict(model, sort=sort)
obj[u"version"] = JSON_SPEC
return json.dumps(obj, allow_nan=False, **kwargs)
def save_yaml_model(model, filename, **kwargs):
"""
Write the cobra model to a file in YAML format.
``kwargs`` are passed on to ``yaml.dump``.
Parameters
----------
model : cobra.Model
The cobra model to represent.
filename : str or file-like
File path or descriptor that the YAML representation should be
written to.
See Also
--------
to_yaml : Return a string representation.
ruamel.yaml.dump : Base function.
"""
obj = model_to_dict(model)
obj["version"] = YAML_SPEC
if isinstance(filename, string_types):
with io.open(filename, "w") as file_handle:
yaml.dump(obj, file_handle, Dumper=yaml.RoundTripDumper, **kwargs)
else:
yaml.dump(obj, filename, Dumper=yaml.RoundTripDumper, **kwargs)
def to_yaml(model, sort=False, **kwargs):
"""
Return the model as a YAML document.
``kwargs`` are passed on to ``yaml.dump``.
Parameters
----------
model : cobra.Model
The cobra model to represent.
sort : bool, optional
Whether to sort the metabolites, reactions, and genes or maintain the
order defined in the model.
Returns
-------
str
String representation of the cobra model as a YAML document.
See Also
--------
save_yaml_model : Write directly to a file.
ruamel.yaml.dump : Base function.
"""
obj = model_to_dict(model, sort=sort)
obj["version"] = YAML_SPEC
return yaml.dump(obj, **kwargs)
def to_json(model, sort=False, **kwargs):
"""
Return the model as a JSON document.
``kwargs`` are passed on to ``json.dumps``.
Parameters
----------
model : cobra.Model
The cobra model to represent.
sort : bool, optional
Whether to sort the metabolites, reactions, and genes or maintain the
order defined in the model.
Returns
-------
str
String representation of the cobra model as a JSON document.
See Also
--------
save_json_model : Write directly to a file.
json.dumps : Base function.
"""
obj = model_to_dict(model, sort=sort)
obj[u"version"] = JSON_SPEC
return json.dumps(obj, allow_nan=False, **kwargs)
def model_to_dict(model):
"""
:param model:
:return:
"""
# Take advantage of cobra's dict serialization for metabolites and
# reactions
obj = cbd.model_to_dict(model)
obj['solver'] = get_solver_string(model)
obj['objective'] = obj_to_dict(model)
# Copy variables, constraints
# obj['var_dict'] = archive_variables(model._var_kinds)
# obj['cons_dict'] = archive_constraints(model._cons_kinds)
obj['variables'] = list(map(var_to_dict, model._var_dict.values()))
obj['constraints'] = list(map(cons_to_dict, model._cons_dict.values()))
is_thermo = False
if isinstance(model, ThermoModel):
obj['kind'] = 'ThermoModel'
obj['thermo_data'] = model.thermo_data #it's a dict
obj['name'] = model.name
obj['temperature'] = model.TEMPERATURE
obj['min_ph'] = model.MIN_pH
obj['max_ph'] = model.MAX_pH
is_thermo = True
# Metabolite and Reaction-level cleanup
for rxn_dict in obj['reactions']:
rxn = model.reactions.get_by_id(rxn_dict['id'])
if is_thermo:
_add_thermo_reaction_info(rxn, rxn_dict)
# Peptides and Thermo
for met_dict in obj['metabolites']:
the_met_id = met_dict['id']
is_peptide = False
if is_thermo and not is_peptide: # peptides have no thermo
the_met = model.metabolites.get_by_id(the_met_id)
_add_thermo_metabolite_info(the_met, met_dict)
met_dict['kind'] = 'Metabolite'
# Relaxation info
try:
obj['relaxation'] = model.relaxation
except AttributeError:
pass
return obj
def save_json_model(model, filename, sort=False, pretty=False, **kwargs):
"""
Write the cobra model to a file in JSON format.
``kwargs`` are passed on to ``json.dump``.
Parameters
----------
model : cobra.Model
The cobra model to represent.
filename : str or file-like
File path or descriptor that the JSON representation should be
written to.
sort : bool, optional
Whether to sort the metabolites, reactions, and genes or maintain the
order defined in the model.
pretty : bool, optional
Whether to format the JSON more compactly (default) or in a more
verbose but easier to read fashion. Can be partially overwritten by the
``kwargs``.
See Also
--------
to_json : Return a string representation.
json.dump : Base function.
"""
obj = model_to_dict(model, sort=sort)
obj[u"version"] = JSON_SPEC
if pretty:
dump_opts = {
"indent": 4,
"separators": (",", ": "),
"sort_keys": True,
"allow_nan": False,
}
else:
dump_opts = {
"indent": 0,
"separators": (",", ":"),
"sort_keys": False,
"allow_nan": False,
}
dump_opts.update(**kwargs)
if isinstance(filename, str):
with open(filename, "w") as file_handle:
json.dump(obj, file_handle, **dump_opts)
else:
json.dump(obj, filename, **dump_opts)
def get_genes_and_gpr(model, gene_outfile, gpr_outfile):
"""Retrieving genes and gene_reaction_rule from GEM.
Arguments
----------
* model: cobra.Model ~ A genome scale metabolic network model for
constructing the enzyme-constrained model.
:return: all genes and gpr in model.
"""
model_dict = model_to_dict(model, sort=False)
genes = pd.DataFrame(model_dict['genes']).set_index(['id'])
genes.to_csv(gene_outfile)
all_gpr = pd.DataFrame(model_dict['reactions']).set_index(['id'])
all_gpr.to_csv(gpr_outfile)
return [genes, all_gpr]
def model_excel(model, output):
from cobra.io.dict import model_to_dict, model_from_dict, metabolite_from_dict, gene_from_dict, reaction_from_dict
from cobra.core import Model
from cobra.io import read_sbml_model, write_sbml_model
import pandas as pd
a = model_to_dict(model, sort=False)
writer = pd.ExcelWriter(output)
#pd.DataFrame(a['compartments']).to_excel(writer,'Sheet1',index=False)
pd.DataFrame(a['metabolites']).to_excel(writer, 'metabolites', index=False)
pd.DataFrame(a['genes']).to_excel(writer, 'genes', index=False)
df_r = pd.DataFrame(a['reactions'])
df_r['reaction_eq'] = df_r.id.apply(lambda x: model.reactions.get_by_id(
x).build_reaction_string(use_metabolite_names=False))
#del df_r['metabolites'] #生成反应方程列后将代谢物列删除，可保留以方便再次读取
df_r.to_excel(writer, 'reactions', index=False)
#df_r.to_excel(writer,'reactions',columns=["id","name","reaction","lower_bound","upper_bound","gene_reaction_rule"],index=False)
writer.save()
def get_genes_and_GPR(model,ID_kcat_file):
GPR = pd.DataFrame()
model_news = model_to_dict(model,sort=False)
df_ID_kcat = pd.read_csv(ID_kcat_file,index_col=0)
genes = pd.DataFrame(model_news['genes'])
genes.drop(['name','annotation'],axis=1,inplace=True)
genes = genes[~genes['id'].isin(['s0001'])]
genes.set_index('id',inplace=True)
genes.to_csv("./genes_file.csv", sep=',')
all_GPR = pd.DataFrame(model_news['reactions'])
all_GPR.drop(['name','metabolites','lower_bound','upper_bound','annotation','objective_coefficient','notes'],axis=1,inplace=True)
all_GPR.to_csv("./all_GPR.csv", sep=',',index=False)
df_all_GPR = pd.read_csv("./all_GPR.csv",index_col=0)
for reaction_id in df_ID_kcat.index:
GPR.loc[reaction_id,'GPR'] = df_all_GPR.loc[reaction_id,'gene_reaction_rule']
GPR.to_csv("./ID_GPR_file.csv", sep=',')
return(genes)
def save_json_model(model, filename, sort=False, pretty=False, **kwargs):
"""
Write the cobra model to a file in JSON format.
``kwargs`` are passed on to ``json.dump``.
Parameters
----------
model : cobra.Model
The cobra model to represent.
filename : str or file-like
File path or descriptor that the JSON representation should be
written to.
sort : bool, optional
Whether to sort the metabolites, reactions, and genes or maintain the
order defined in the model.
pretty : bool, optional
Whether to format the JSON more compactly (default) or in a more
verbose but easier to read fashion. Can be partially overwritten by the
``kwargs``.
See Also
--------
to_json : Return a string representation.
json.dump : Base function.
"""
obj = model_to_dict(model, sort=sort)
obj[u"version"] = JSON_SPEC
if pretty:
dump_opts = {
"indent": 4, "separators": (",", ": "), "sort_keys": True,
"allow_nan": False}
else:
dump_opts = {
"indent": 0, "separators": (",", ":"), "sort_keys": False,
"allow_nan": False}
dump_opts.update(**kwargs)
if isinstance(filename, string_types):
with open(filename, "w") as file_handle:
json.dump(obj, file_handle, **dump_opts)
else:
json.dump(obj, filename, **dump_opts)
def to_json(model, **kwargs):
"""
Return the model as a JSON document.
``kwargs`` are passed on to ``json.dumps``.
Parameters
----------
model : cobra.Model
The cobra model to represent.
Returns
-------
str
String representation of the cobra model as a JSON document.
See Also
--------
save_json_model : Write directly to a file.
json.dumps : Base function.
"""
obj = model_to_dict(model)
obj[u"version"] = JSON_SPEC
return json.dumps(obj, allow_nan=False, **kwargs)
def to_yaml(model, **kwargs):
"""
Return the model as a YAML document.
``kwargs`` are passed on to ``yaml.dump``.
Parameters
----------
model : cobra.Model
The cobra model to represent.
Returns
-------
str
String representation of the cobra model as a YAML document.
See Also
--------
save_yaml_model : Write directly to a file.
ruamel.yaml.dump : Base function.
"""
obj = model_to_dict(model)
obj["version"] = YAML_SPEC
return yaml.dump(obj, Dumper=yaml.RoundTripDumper, **kwargs)
def model_to_dict(model):
"""
:param model:
:return:
"""
# Take advantage of cobra's dict serialization for metabolites and
# reactions
obj = cbd.model_to_dict(model)
obj['solver'] = get_solver_string(model)
obj['objective'] = obj_to_dict(model)
# Copy variables, constraints
# obj['var_dict'] = archive_variables(model._var_kinds)
# obj['cons_dict'] = archive_constraints(model._cons_kinds)
obj['variables'] = list(map(var_to_dict, model._var_dict.values()))
obj['constraints'] = list(map(cons_to_dict, model._cons_dict.values()))
is_thermo = False
is_me = False
if isinstance(model, ThermoModel):
obj['kind'] = 'ThermoModel'
obj['thermo_data'] = model.thermo_data #it's a dict
obj['name'] = model.name
obj['temperature'] = model.TEMPERATURE
obj['min_ph'] = model.MIN_pH
obj['max_ph'] = model.MAX_pH
is_thermo = True
# Relaxation info
try:
obj['relaxation'] = model.relaxation
except AttributeError:
pass
if isinstance(model, MEModel):
# Convenience attributes
# obj['_mu'] = model.mu.name
# obj['compositions'] = archive_compositions(model.compositions)
# obj['coupling_dict'] = archive_coupling_dict(model.coupling_dict)
obj['mu_bins'] = model.mu_bins
obj['essentials'] = model.essentials
obj['rna_nucleotides'] = model.rna_nucleotides
obj['rna_nucleotides_mp'] = model.rna_nucleotides_mp
try:
obj['dna_nucleotides'] = model.dna_nucleotides
except AttributeError:
# DNA has not been added
pass
obj['aa_dict'] = model.aa_dict
# Growth
obj['growth_reaction'] = model.growth_reaction.id
# Genes
obj['expressed_genes'] = list(
map(expressed_gene_to_dict,
[g for g in model.genes if isinstance(g, ExpressedGene)]))
# Enzymes
obj['enzymes'] = list(map(enzyme_to_dict, model.enzymes))
# mRNAs
obj['mrnas'] = list(map(mrna_to_dict, model.mrnas))
# tRNAs
obj['trna_dict'] = archive_trna_dict(model)
# Ribosome
obj['ribosome'] = ribosome_to_dict(model.ribosome)
# RNAP
obj['rnap'] = rnap_to_dict(model.rnap)
try:
obj['dna'] = dna_to_dict(model.dna)
except AttributeError:
# DNA has not been added
pass
obj['kind'] = 'MEModel'
is_me = True
if isinstance(model, ThermoMEModel):
obj['kind'] = 'ThermoMEModel'
is_me = True
# Metabolite and Reaction-level cleanup
for rxn_dict in obj['reactions']:
rxn = model.reactions.get_by_id(rxn_dict['id'])
if is_me:
_add_me_reaction_info(rxn, rxn_dict)
if is_thermo:
_add_thermo_reaction_info(rxn, rxn_dict)
# Peptides and Thermo
for met_dict in obj['metabolites']:
the_met_id = met_dict['id']
met_dict['kind'] = 'Metabolite'
the_met = model.metabolites.get_by_id(the_met_id)
is_me_met = False
if is_me:
if the_met_id in model.peptides:
met_dict['kind'] = 'Peptide'
met_dict['gene_id'] = the_met._gene_id
if the_met._molecular_weight_override:
met_dict['molecular_weight_override'] = \
the_met._molecular_weight_override
is_me_met = True
if the_met_id in model.rrnas:
met_dict['kind'] = 'rRNA'
is_me_met = True
if is_thermo and not is_me_met: # peptides have no thermo
_add_thermo_metabolite_info(the_met, rxn_dict)
find_genes_from_dict(model, obj)
return obj
