def convert(the_map,
model,
map_name=None,
map_description=None,
reaction_id_mapping=None,
metabolite_id_mapping=None,
gene_id_mapping=None,
debug=False):
"""Convert an Escher map to the latest format using the COBRA model to update
content. Returns a new map.
Arguments
---------
the_map: An Escher map loaded as a Python object (e.g. json.load('my_map.json')).
model: A COBRA model.
map_name: A name for the map. If a name is already present, this name
overrides it.
map_description: A description for the map. If a name is already present,
this name overrides it.
reaction_id_mapping: A dictionary with existing reaction IDs as keys and the
new reaction IDs as values.
metabolite_id_mapping: A dictionary with existing metabolite IDs as keys and the
new metabolite IDs as values.
gene_id_mapping: A dictionary with existing gene IDs as keys and the new
gene IDs as values.
debug: Check the map against the schema at some intermediate steps.
"""
# make sure everything is up-to-date
new_map = old_map_to_new_schema(the_map,
map_name=map_name,
map_description=map_description)
if debug:
validate_map(new_map)
# apply the ids mappings
apply_id_mappings(new_map, reaction_id_mapping, metabolite_id_mapping,
gene_id_mapping)
if debug:
validate_map(new_map)
# apply the new model
apply_cobra_model_to_map(new_map, model)
validate_map(new_map)
return new_map
def convert(the_map, model, map_name=None, map_description=None,
reaction_id_mapping=None, metabolite_id_mapping=None,
gene_id_mapping=None, debug=False):
"""Convert an Escher map to the latest format using the COBRA model to update
content. Returns a new map.
Arguments
---------
the_map: An Escher map loaded as a Python object (e.g. json.load('my_map.json')).
model: A COBRA model.
map_name: A name for the map. If a name is already present, this name
overrides it.
map_description: A description for the map. If a name is already present,
this name overrides it.
reaction_id_mapping: A dictionary with existing reaction IDs as keys and the
new reaction IDs as values.
metabolite_id_mapping: A dictionary with existing metabolite IDs as keys and the
new metabolite IDs as values.
gene_id_mapping: A dictionary with existing gene IDs as keys and the new
gene IDs as values.
debug: Check the map against the schema at some intermediate steps.
"""
# make sure everything is up-to-date
new_map = old_map_to_new_schema(the_map, map_name=map_name,
map_description=map_description)
if debug:
validate_map(new_map)
# apply the ids mappings
apply_id_mappings(new_map, reaction_id_mapping, metabolite_id_mapping,
gene_id_mapping)
if debug:
validate_map(new_map)
# apply the new model
apply_cobra_model_to_map(new_map, model)
validate_map(new_map)
return new_map
def test_validate_map():
the_map = [{ 'map_name': 'carbohydrate metabolism',
'map_id': 'h_sapiens_carb',
'map_description': 'A map of central carbon→ metabolism',
'homepage': 'https://escher.github.io',
'schema': 'https://escher.github.io/escher/jsonschema/1-0-0#'
},
{ 'reactions': { '1': {'name': 'glyceraldehyde-3-phosphate dehydrogenase',
'bigg_id': 'GAPD',
'reversibility': True,
'label_x': 0,
'label_y': 0,
'gene_reaction_rule': 'b1779',
'genes': [{ 'bigg_id': 'b1779', 'name': 'gapA' }],
'metabolites': [{ 'bigg_id': 'g3p_c', 'coefficient': -1 }],
'segments': { '2': { 'from_node_id': '0',
'to_node_id': '1',
'b1': None,
'b2': None } } } },
'nodes': { '0': { 'node_type': 'metabolite',
'x': 1,
'y': 2,
'bigg_id': 'g3p_c',
'name': 'glyceraldehyde-3-phosphate cytosolic',
'label_x': 3,
'label_y': 3,
'node_is_primary': True },
'1': { 'node_type': 'multimarker',
'x': 10,
'y': 12.3 } },
'text_labels': {},
'canvas': {'x': 1208.24,
'y':794.55,
'width':10402.35,
'height':13224.91}
}]
validate_map(the_map)
# missing node
new_map = deepcopy(the_map)
del new_map[1]['nodes']['1']
with raises(Exception) as e:
validate_map(new_map)
print(e)
assert 'No nodes for segments' in str(e.value)
# zero coefficient
new_map = deepcopy(the_map)
new_map[1]['reactions']['1']['metabolites'][0]['coefficient'] = 0
with raises(Exception) as e:
validate_map(new_map)
print(e)
assert 'No non-zero stoichiometry for a connected metabolite node' in str(e.value)
# # midmarker connected to metabolite
# new_map = deepcopy(the_map)
# new_map[1]['nodes']['1']['node_type'] = 'midmarker'
# with raises(Exception) as e:
# validate_map(new_map)
# print(e)
# assert 'Segments connect midmarkers to metabolites' in str(e.value)
# No gene name for gene in gene_reaction_rule
new_map = deepcopy(the_map)
del new_map[1]['reactions']['1']['genes'][0]['name']
with raises(Exception) as e:
validate_map(new_map)
print(e)
assert 'No gene name for gene in gene_reaction_rule' in str(e.value)
def convert(map, model):
# check for new, 2-level maps
has_head = isinstance(map, list) and len(map) == 2
if has_head:
map_body = map[1]
else:
map_body = map
# add missing elements
for k in ['nodes', 'reactions', 'text_labels']:
if k not in map_body or len(map_body[k]) == 0:
map_body[k] = {}
# default canvas
if 'canvas' not in map_body:
map_body['canvas'] = { 'x': -1440,
'y': -775,
'width': 4320,
'height': 2325 }
# keep track of deleted nodes and reactions
nodes_to_delete = set()
reactions_to_delete = set()
nodes_with_segments = set()
# nodes
for id, node in map_body['nodes'].items():
# follow rules for type
# metabolites
if node['node_type'] == 'metabolite':
# no bigg_id
if not 'bigg_id' in node:
print('No bigg_id for node %s. Deleting.' % id)
nodes_to_delete.add(id)
# unsupported attributes
for key in list(node.keys()):
if not key in ["node_type", "x", "y", "bigg_id", "name",
"label_x", "label_y", "node_is_primary"]:
del node[key]
# find the metabolite
try:
cobra_metabolite = model.metabolites.get_by_id(node['bigg_id'])
except KeyError:
print('Could not find metabolite %s in model. Deleting.' % node['bigg_id'])
nodes_to_delete.add(id)
continue
# apply new display names
node['name'] = cobra_metabolite.name
# node_is_primary defaults to False
if not 'node_is_primary' in node or node['node_is_primary'] not in [True, False]:
node['node_is_primary'] = False
# markers
elif node['node_type'] in ['multimarker', 'midmarker']:
# unsupported attributes
for key in list(node.keys()):
if not key in ["node_type", "x", "y"]:
del node[key]
# invalid node_type
else:
nodes_to_delete.add(id)
# update reactions
for id, reaction in map_body['reactions'].items():
# missing attributes
will_delete = False
for k in ["bigg_id", "segments", "label_x", "label_y"]:
if not k in reaction:
print('No %s for reaction %s. Deleting.' % (k, id))
reactions_to_delete.add(id)
will_delete = True
if will_delete:
continue
# unsupported attributes
for key in list(reaction.keys()):
if not key in ["name", "bigg_id","reversibility",
"label_x", "label_y", "gene_reaction_rule",
"genes", "metabolites", "segments"]:
del reaction[key]
# cast attributes
for k in ['label_x', 'label_y']:
reaction[k] = float(reaction[k])
# unsupported attributes in segments
for s_id, segment in reaction['segments'].items():
for key in list(segment.keys()):
if not key in ["from_node_id", "to_node_id", "b1", "b2"]:
del segment[key]
# cast attributes
for k in ['b1', 'b2']:
if segment[k] is not None and (segment[k]['x'] is None or segment[k]['y'] is None):
segment[k] = None
# keep track of nodes that have appeared here
for key in ['from_node_id', 'to_node_id']:
try:
nodes_with_segments.add(segment[key])
except KeyError:
pass
# get reaction
try:
cobra_reaction = model.reactions.get_by_id(reaction['bigg_id'])
except KeyError:
print('Could not find reaction %s in model. Deleting.' % reaction['bigg_id'])
reactions_to_delete.add(id)
continue
reaction['gene_reaction_rule'] = cobra_reaction.gene_reaction_rule
reaction['reversibility'] = (cobra_reaction.lower_bound < 0 and cobra_reaction.upper_bound > 0)
# reverse metabolites if reaction runs in reverse
rev_mult = (-1 if
(cobra_reaction.lower_bound < 0 and cobra_reaction.upper_bound <= 0)
else 1)
# use metabolites from reaction
reaction['metabolites'] = [{'bigg_id': met.id, 'coefficient': coeff * rev_mult}
for met, coeff in
cobra_reaction.metabolites.items()]
reaction['name'] = cobra_reaction.name
reaction['genes'] = []
for gene in genes_for_gene_reaction_rule(reaction['gene_reaction_rule']):
try:
cobra_gene = model.genes.get_by_id(gene)
except KeyError:
print('Could not find gene %s in model. Setting name to ID.')
reaction['genes'].append({'bigg_id': gene, 'name': gene})
continue
reaction['genes'].append({'bigg_id': gene, 'name': cobra_gene.name})
# remove any lost segments
reaction['segments'] = {id: seg for id, seg in reaction['segments'].items()
if ((seg['to_node_id'] in map_body['nodes'] and seg['to_node_id'] not in nodes_to_delete) and
(seg['from_node_id'] in map_body['nodes'] and seg['from_node_id'] not in nodes_to_delete))}
# delete those reactions
for reaction_id in reactions_to_delete:
del map_body['reactions'][reaction_id]
# delete those nodes
for node_id in nodes_to_delete:
del map_body['nodes'][node_id]
# delete any nodes with no segment
for node_id in list(map_body['nodes'].keys()):
if node_id not in nodes_with_segments:
# may not be there, if previously deleted
try:
del map_body['nodes'][node_id]
print('No segments for node %s. Deleting' % node_id)
except KeyError:
pass
# text labels
for id, text_label in map_body['text_labels'].items():
# unsupported attributes
for key in list(text_label.keys()):
if not key in ["x", "y", "text"]:
del text_label[key]
# canvas
# unsupported attributes
for key in list(map_body['canvas'].keys()):
if not key in ["x", "y", "width", "height"]:
del map_body['canvas'][key]
# delete unsupported elements
for key in list(map_body.keys()):
if not key in ["nodes", "reactions", "text_labels", "canvas"]:
del map_body[key]
header = {
"schema": "https://escher.github.io/escher/jsonschema/1-0-0#",
"homepage": "https://escher.github.io",
"map_name": "",
"map_id": "",
"map_description": ""
}
if has_head:
for key, value in map[0].items():
if key in ['schema', 'homepage']: continue
header[key] = value
the_map = [header, map_body]
validate_map(the_map)
return the_map
def test_validate_map():
the_map = [{ 'map_name': 'carbohydrate metabolism',
'map_id': 'h_sapiens_carb',
'map_description': 'A map of central carbon→ metabolism',
'homepage': 'https://escher.github.io',
'schema': 'https://escher.github.io/escher/jsonschema/1-0-0#'
},
{ 'reactions': { '1': {'name': 'glyceraldehyde-3-phosphate dehydrogenase',
'bigg_id': 'GAPD',
'reversibility': True,
'label_x': 0,
'label_y': 0,
'gene_reaction_rule': 'b1779',
'genes': [{ 'bigg_id': 'b1779', 'name': 'gapA' }],
'metabolites': [{ 'bigg_id': 'g3p_c', 'coefficient': -1 }],
'segments': { '2': { 'from_node_id': '0',
'to_node_id': '1',
'b1': None,
'b2': None } } } },
'nodes': { '0': { 'node_type': 'metabolite',
'x': 1,
'y': 2,
'bigg_id': 'g3p_c',
'name': 'glyceraldehyde-3-phosphate cytosolic',
'label_x': 3,
'label_y': 3,
'node_is_primary': True },
'1': { 'node_type': 'multimarker',
'x': 10,
'y': 12.3 } },
'text_labels': {},
'canvas': {'x': 1208.24,
'y':794.55,
'width':10402.35,
'height':13224.91}
}]
validate_map(the_map)
# missing node
new_map = deepcopy(the_map)
del new_map[1]['nodes']['1']
with raises(Exception) as e:
validate_map(new_map)
print(e)
assert 'No nodes for segments' in str(e.value)
# zero coefficient
new_map = deepcopy(the_map)
new_map[1]['reactions']['1']['metabolites'][0]['coefficient'] = 0
with raises(Exception) as e:
validate_map(new_map)
print(e)
assert 'No non-zero stoichiometry for a connected metabolite node' in str(e.value)
# # midmarker connected to metabolite
# new_map = deepcopy(the_map)
# new_map[1]['nodes']['1']['node_type'] = 'midmarker'
# with raises(Exception) as e:
# validate_map(new_map)
# print(e)
# assert 'Segments connect midmarkers to metabolites' in str(e.value)
# No gene name for gene in gene_reaction_rule
new_map = deepcopy(the_map)
del new_map[1]['reactions']['1']['genes'][0]['name']
with raises(Exception) as e:
validate_map(new_map)
print(e)
assert 'No gene name for gene in gene_reaction_rule' in str(e.value)
def convert(map, model):
# check for new, 2-level maps
has_head = isinstance(map, list) and len(map) == 2
if has_head:
map_body = map[1]
else:
map_body = map
# add missing elements
for k in ['nodes', 'reactions', 'text_labels']:
if k not in map_body or len(map_body[k]) == 0:
map_body[k] = {}
# default canvas
if 'canvas' not in map_body:
map_body['canvas'] = {
'x': -1440,
'y': -775,
'width': 4320,
'height': 2325
}
# keep track of deleted nodes and reactions
nodes_to_delete = set()
reactions_to_delete = set()
nodes_with_segments = set()
# nodes
for id, node in map_body['nodes'].items():
# follow rules for type
# metabolites
if node['node_type'] == 'metabolite':
# no bigg_id
if not 'bigg_id' in node:
print('No bigg_id for node %s. Deleting.' % id)
nodes_to_delete.add(id)
# unsupported attributes
for key in list(node.keys()):
if not key in [
"node_type", "x", "y", "bigg_id", "name", "label_x",
"label_y", "node_is_primary"
]:
del node[key]
# find the metabolite
try:
cobra_metabolite = model.metabolites.get_by_id(node['bigg_id'])
except KeyError:
print('Could not find metabolite %s in model. Deleting.' %
node['bigg_id'])
nodes_to_delete.add(id)
continue
# apply new display names
node['name'] = cobra_metabolite.name
# node_is_primary defaults to False
if not 'node_is_primary' in node or node[
'node_is_primary'] not in [True, False]:
node['node_is_primary'] = False
# markers
elif node['node_type'] in ['multimarker', 'midmarker']:
# unsupported attributes
for key in list(node.keys()):
if not key in ["node_type", "x", "y"]:
del node[key]
# invalid node_type
else:
nodes_to_delete.add(id)
# update reactions
for id, reaction in map_body['reactions'].items():
# missing attributes
will_delete = False
for k in ["bigg_id", "segments", "label_x", "label_y"]:
if not k in reaction:
print('No %s for reaction %s. Deleting.' % (k, id))
reactions_to_delete.add(id)
will_delete = True
if will_delete:
continue
# unsupported attributes
for key in list(reaction.keys()):
if not key in [
"name", "bigg_id", "reversibility", "label_x", "label_y",
"gene_reaction_rule", "genes", "metabolites", "segments"
]:
del reaction[key]
# cast attributes
for k in ['label_x', 'label_y']:
reaction[k] = float(reaction[k])
# unsupported attributes in segments
for s_id, segment in reaction['segments'].items():
for key in list(segment.keys()):
if not key in ["from_node_id", "to_node_id", "b1", "b2"]:
del segment[key]
# cast attributes
for k in ['b1', 'b2']:
if segment[k] is not None and (segment[k]['x'] is None
or segment[k]['y'] is None):
segment[k] = None
# keep track of nodes that have appeared here
for key in ['from_node_id', 'to_node_id']:
try:
nodes_with_segments.add(segment[key])
except KeyError:
pass
# get reaction
try:
cobra_reaction = model.reactions.get_by_id(reaction['bigg_id'])
except KeyError:
print('Could not find reaction %s in model. Deleting.' %
reaction['bigg_id'])
reactions_to_delete.add(id)
continue
reaction['gene_reaction_rule'] = cobra_reaction.gene_reaction_rule
reaction['reversibility'] = (cobra_reaction.lower_bound < 0
and cobra_reaction.upper_bound > 0)
# reverse metabolites if reaction runs in reverse
rev_mult = (-1 if (cobra_reaction.lower_bound < 0
and cobra_reaction.upper_bound <= 0) else 1)
# use metabolites from reaction
reaction['metabolites'] = [{
'bigg_id': met.id,
'coefficient': coeff * rev_mult
} for met, coeff in cobra_reaction.metabolites.items()]
reaction['name'] = cobra_reaction.name
reaction['genes'] = []
for gene in genes_for_gene_reaction_rule(
reaction['gene_reaction_rule']):
try:
cobra_gene = model.genes.get_by_id(gene)
except KeyError:
print('Could not find gene %s in model. Setting name to ID.')
reaction['genes'].append({'bigg_id': gene, 'name': gene})
continue
reaction['genes'].append({
'bigg_id': gene,
'name': cobra_gene.name
})
# remove any lost segments
reaction['segments'] = {
id: seg
for id, seg in reaction['segments'].items()
if ((seg['to_node_id'] in map_body['nodes']
and seg['to_node_id'] not in nodes_to_delete) and (
seg['from_node_id'] in map_body['nodes']
and seg['from_node_id'] not in nodes_to_delete))
}
# delete those reactions
for reaction_id in reactions_to_delete:
del map_body['reactions'][reaction_id]
# delete those nodes
for node_id in nodes_to_delete:
del map_body['nodes'][node_id]
# delete any nodes with no segment
for node_id in list(map_body['nodes'].keys()):
if node_id not in nodes_with_segments:
# may not be there, if previously deleted
try:
del map_body['nodes'][node_id]
print('No segments for node %s. Deleting' % node_id)
except KeyError:
pass
# text labels
for id, text_label in map_body['text_labels'].items():
# unsupported attributes
for key in list(text_label.keys()):
if not key in ["x", "y", "text"]:
del text_label[key]
# canvas
# unsupported attributes
for key in list(map_body['canvas'].keys()):
if not key in ["x", "y", "width", "height"]:
del map_body['canvas'][key]
# delete unsupported elements
for key in list(map_body.keys()):
if not key in ["nodes", "reactions", "text_labels", "canvas"]:
del map_body[key]
header = {
"schema": "https://escher.github.io/escher/jsonschema/1-0-0#",
"homepage": "https://escher.github.io",
"map_name": "",
"map_id": "",
"map_description": ""
}
if has_head:
for key, value in map[0].items():
if key in ['schema', 'homepage']: continue
header[key] = value
the_map = [header, map_body]
validate_map(the_map)
return the_map