def test_flux_map_knockout(simple_model):
simple_model.objective = simple_model.reactions.R4
simple_model.reactions.R8.knock_out()
simple_model.optimize()
svg = flux_map(simple_model, figsize=(300, 250))
assert svg is not None
def test_flux_map(simple_model):
svg = flux_map(simple_model,
display_name_format=lambda x: str(x.id),
figsize=(300, 250),
flux_dict={rxn.id: None
for rxn in simple_model.reactions})
assert svg is not None
from cobra.io import load_json_model
from d3flux import flux_map
new_model = load_json_model('simple_model.json')
new_model.objective = new_model.reactions.R4
# new_model.reactions.R8.knock_out()
new_model.reactions.R6.knock_out()
new_model.optimize()
new_model.metabolites.B.notes['map_info']['align'] = 'left'
new_model.metabolites.P.notes['map_info']['align'] = 'lower center'
new_model.metabolites.C.notes['map_info']['align'] = 'upper right'
new_model.reactions.R5.bounds = (-1000, 1000)
html = flux_map(new_model, figsize=(300, 250), inactive_alpha=0.5)
with open('test.html', 'w') as f:
f.write(
'<!DOCTYPE html> <html> <head> <title>Test d3flux page</title> <script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.2/require.min.js" integrity="sha256-Vjusm6Kh2U7/tb6jBh+MOfxnaf2TWsTph34bMKhC1Qc=" crossorigin="anonymous"></script> <script src="https://code.jquery.com/jquery-3.1.1.min.js" integrity="sha256-hVVnYaiADRTO2PzUGmuLJr8BLUSjGIZsDYGmIJLv2b8=" crossorigin="anonymous"></script> <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"> </head> <body>'
)
f.write(html.data)
f.write('</body> </html>')
def print_summary(scope, tar_met, pathways, cut_len, cyclic, namemap, src_met, seed_met, G, all_tar2src, diff_tar2src):
# global pathway1
# pathway1 = create_pathway(seed_met, cut_len, src_met, tar_met, 0, most_diff, namemap, G)
# global pathway2
# pathway2 = create_pathway(seed_met, cut_len, src_met, tar_met, 1, most_diff, namemap, G)
global pathsHTML
global pathsUnion
pathsHTML = []
labels = []
pathsUnion = []
labelsUnion = []
labelsSummary = []
len_scopes = []
cut_branched_pathss = []
all_cnts = []
cut_cnts = []
cut_cyclics = []
minstepss = []
for i in range(len(tar_met)):
for j in range(len(src_met)):
labelSummary = "%s %s to %s summary"%("_".join(modids), src_met[j], tar_met[i])
labelsSummary.append(labelSummary)
if len(diff_tar2src[tar_met[i]][src_met[j]]) == 0:
if len(all_tar2src[tar_met[i]][src_met[j]]) == 0:
print('No pathway found for %s to %s'%(src_met[j],tar_met[i]))
pathsHTML.append(None)
label = "%s %s to %s no pathway"%("_".join(modids), src_met[j], tar_met[i])
labels.append(label)
pathsUnion.append(None)
labelsUnion.append(label)
len_scopes.append(len(scope))
cut_branched_paths = len(all_tar2src[tar_met[i]][src_met[j]])
cut_branched_pathss.append(cut_branched_paths)
all_cnts.append(None)
cut_cnts.append(None)
cut_cyclics.append(None)
minstepss.append(None)
else:
print('just one pathway found for %s to %s'%(src_met[j],tar_met[i]))
k = 0
r = all_tar2src[tar_met[i]][src_met[j]][k]
d = create_pathway(namemap, G, r)
jsonFileName = '%s_%s to %s_just one pathway.json'%("_".join(modids), src_met[j], tar_met[i])
with open(os.path.join(app.config['UPLOAD_PATH'], jsonFileName), 'w') as fp:
json.dump(d, fp, separators=(',',':'))
mod = cobra.io.json.load_json_model(os.path.join(app.config['UPLOAD_PATH'], jsonFileName))
page = flux_map(mod, display_name_format=lambda x: str(x.id), figsize=(1024,500),flux_dict={rxn.id: None for rxn in mod.reactions})
pathsHTML.append(page)
label = jsonFileName
labels.append(label)
pathsUnion.append(page)
labelsUnion.append(label)
pred = G.predecessors
succ = G.successors
all_pathways_count = []
path_count = []
cyclic_pathway_count = []
all_reactions_involved = []
len_scope = len(scope)
len_scopes.append(len_scope)
cut_branched_paths = len(all_tar2src[tar_met[i]][src_met[j]])
cut_branched_pathss.append(cut_branched_paths)
for plen in pathways[tar_met[i]]:
all_pathways_count.append(len(pathways[tar_met[i]][plen]))
if plen <= int(cut_len):
path_count.append(len(pathways[tar_met[i]][plen]))
for p in pathways[tar_met[i]][plen]:
for reactions in p:
all_reactions_involved.append(reactions)
if tar_met[i] in cyclic:
for plen in cyclic[tar_met[i]]:
if plen <= int(cut_len):
cyclic_pathway_count.append(len(cyclic[tar_met[i]][plen]))
all_cnt = sum(all_pathways_count)
all_cnts.append(all_cnt)
cut_cnt = sum(path_count)
cut_cnts.append(cut_cnt)
cut_cyclic = sum(cyclic_pathway_count)
cut_cyclics.append(cut_cyclic)
minsteps = min(pathways[tar_met[i]])
minstepss.append(minsteps)
else:
wt = {}
for a in range(len(all_tar2src[tar_met[i]][src_met[j]])):
for b in range(len(all_tar2src[tar_met[i]][src_met[j]][a])):
wt[all_tar2src[tar_met[i]][src_met[j]][a][b].replace(" ","")] = 0
for a in range(len(all_tar2src[tar_met[i]][src_met[j]])):
for b in range(len(all_tar2src[tar_met[i]][src_met[j]][a])):
wt[all_tar2src[tar_met[i]][src_met[j]][a][b].replace(" ","")] += 1
rUnion = set()
for a in range(len(all_tar2src[tar_met[i]][src_met[j]])):
rUnion.update(all_tar2src[tar_met[i]][src_met[j]][a])
rUnion = list(rUnion)
dUnion = create_pathway(namemap, G, rUnion)
jsonFileName = '%s_%s to %s_UNION.json'%("_".join(modids), src_met[j], tar_met[i])
with open(os.path.join(app.config['UPLOAD_PATH'], jsonFileName), 'w') as fp:
json.dump(dUnion, fp, separators=(',',':'))
modUnion = cobra.io.json.load_json_model(os.path.join(app.config['UPLOAD_PATH'], jsonFileName))
solution = modUnion.optimize()
a = 0
for reacts in modUnion.reactions:
rs = str(reacts.id)
solution.fluxes[a] = wt[rs]
a = a+1
pageUnion = flux_map(modUnion, display_name_format=lambda x: str(x.id), figsize=(1024,500),flux_dict= solution)
pathsUnion.append(pageUnion)
labelUnion = jsonFileName
labelsUnion.append(labelUnion)
pred = G.predecessors
succ = G.successors
all_pathways_count = []
path_count = []
cyclic_pathway_count = []
all_reactions_involved = []
len_scope = len(scope)
len_scopes.append(len_scope)
cut_branched_paths = len(all_tar2src[tar_met[i]][src_met[j]])
cut_branched_pathss.append(cut_branched_paths)
for plen in pathways[tar_met[i]]:
all_pathways_count.append(len(pathways[tar_met[i]][plen]))
if plen <= int(cut_len):
path_count.append(len(pathways[tar_met[i]][plen]))
for p in pathways[tar_met[i]][plen]:
for reactions in p:
all_reactions_involved.append(reactions)
if tar_met[i] in cyclic:
for plen in cyclic[tar_met[i]]:
if plen <= int(cut_len):
cyclic_pathway_count.append(len(cyclic[tar_met[i]][plen]))
all_cnt = sum(all_pathways_count)
all_cnts.append(all_cnt)
cut_cnt = sum(path_count)
cut_cnts.append(cut_cnt)
cut_cyclic = sum(cyclic_pathway_count)
cut_cyclics.append(cut_cyclic)
minsteps = min(pathways[tar_met[i]])
minstepss.append(minsteps)
for k in range(2):
print('Most different pathway combination found for %s to %s'%(src_met[j],tar_met[i]))
r = diff_tar2src[tar_met[i]][src_met[j]][k]
d = create_pathway(namemap, G, r)
jsonFileName = '%s_%s to %s_%i.json'%("_".join(modids), src_met[j], tar_met[i], k)
with open(os.path.join(app.config['UPLOAD_PATH'], jsonFileName), 'w') as fp:
json.dump(d, fp, separators=(',',':'))
mod = cobra.io.json.load_json_model(os.path.join(app.config['UPLOAD_PATH'], jsonFileName))
page = flux_map(mod, display_name_format=lambda x: str(x.id), figsize=(1024,500),flux_dict={rxn.id: None for rxn in mod.reactions})
pathsHTML.append(page)
label = jsonFileName
labels.append(label)
return render_template('combi.html', pathsHTML = pathsHTML, labels = labels, pathsUnion = pathsUnion, labelsUnion = labelsUnion, labelsSummary = labelsSummary, len_scopes = len_scopes, cut_branched_pathss = cut_branched_pathss, all_cnts = all_cnts, cut_cnts = cut_cnts, cut_cyclics = cut_cyclics, minstepss = minstepss, cut_len = cut_len, tar_met = tar_met)