def make_welcome_page(self, mailaddr, filename):
db = Database()
try:
prob = db.get_properties('maildata')
user_name = prob[mailaddr]
writer = HtmlWriter(open(filename, mode='w'))
writer.title('Welcome to ' + user_name + 'is page!')
writer.paragraph(user_name + 'のページへようこそ。')
writer.paragraph('メール待っていますね。')
writer.mailto(mailaddr, user_name)
writer.close()
print(filename + ' ' + 'is created for' + ' ' + mailaddr + ' ' + '(' + user_name + ')')
except IOError as e:
logging.exception(e)
def make_welcome_page(self, mailaddr, filename):
db = Database()
try:
prob = db.get_properties('maildata')
user_name = prob[mailaddr]
writer = HtmlWriter(open(filename, mode='w'))
writer.title('Welcome to ' + user_name + 'is page!')
writer.paragraph(user_name + 'のページへようこそ。')
writer.paragraph('メール待っていますね。')
writer.mailto(mailaddr, user_name)
writer.close()
print(filename + ' ' + 'is created for' + mailaddr + ' ' + '(' +
user_name + ')')
except IOError as e:
logging.exception(e)
ax_met = fig2.add_subplot(1, 2, 2, xscale="log", yscale="log")
ax_met.set_title("eCF(1SP) Metabolite concentrations")
model.ValidateMetaboliteConcentrations(lnC_ECM, ax_met)
model.ValidateEnzymeConcentrations(lnC_ECM, ax_enz)
fig2.show()
html.write("<p>\n")
html.write("<b>Experiment name:</b> %s</br>\n" % exp_name)
html.embed_matplotlib_figure(fig1)
html.write("</p><p>\n")
html.embed_matplotlib_figure(fig2)
html.write("</p><p>\n")
model.WriteHtmlTables(lnC_ECM, html)
html.write("</p>\n")
html.close()
# make plots also in linear scale just for fun
fig3 = plt.figure(figsize=(14, 6))
fig3.suptitle("Valdiation")
ax_enz = fig3.add_subplot(1, 2, 1, xscale="linear", yscale="linear")
ax_enz.set_title("eCF3(1SP) Enzyme concentrations")
ax_met = fig3.add_subplot(1, 2, 2, xscale="linear", yscale="linear")
ax_met.set_title("eCF3(1SP) Metabolite concentrations")
model.ValidateMetaboliteConcentrations(lnC_ECM, ax_met, scale="linear")
model.ValidateEnzymeConcentrations(lnC_ECM, ax_enz, scale="linear")
fig3.show()
from cobra.io.sbml import create_cobra_model_from_sbml_file
from html_writer import HtmlWriter
import analysis_toolbox
main_html = HtmlWriter('res/fba.html')
main_html.write('<title>FBA</title>')
main_html.write('<h1>FBA</h1>\n')
model = create_cobra_model_from_sbml_file('data/iJO1366.xml')
main_html.write('</ul>\n')
print("Running standard FBA...")
solution = model.optimize()
if solution.status is not None:
# write the flux summary for the knockout model as HTML
analysis_toolbox.model_summary(model, solution, main_html)
main_html.close()
