def go_term_info(goid=None):
if goid is None:
flash("That page needs a GOID")
return redirect(url_for("homepage"))
go_info = es.go_info(goid)
genes = es.go_to_gene(goid)
if go_info is None or genes is None:
if go_info is None:
flash("You need to implement <code>go_info()</code>")
if genes is None:
flash("You need to implement <code>go_to_gene()</code>")
return redirect(url_for('homepage'))
genes = [(gene, es.gene_name(gene)) for gene in es.go_to_gene(goid)]
local_network = hs.go_network(goid, True, 1)
if local_network is None:
flash("You could maybe implement <code>go_network()</code>")
elif len(local_network['nodes']) > 1000:
flash("Too many nodes to plot a network, forget it")
local_network = {'nodes': [], 'links': []}
return render_template("go_term.html", go_info=go_info, genes=genes,
local_network=local_network)
def go_term_info(goid):
go_info = es.go_info(goid)
genes = es.go_to_gene(goid)
if go_info is None or genes is None:
if go_info is None:
flash("You need to implement <code>go_info()</code>")
if genes is None:
flash("You need to implement <code>go_to_gene()</code>")
return redirect(url_for('homepage'))
genes = [(gene, es.gene_name(gene)) for gene in es.go_to_gene(goid)]
return render_template("go_term.html", go_info=go_info, genes=genes)
def enrichment(exp, aspect, n=100):
aspect = set(aspect)
if not aspect.intersection('CFP'):
flash("That's not a valid aspect, try C, F, and/or P")
return redirect(url_for('experiment', exp=exp))
exp_data = es.experiment()
if exp_data is not None:
exp_data = exp_data[exp]
else:
flash("You need to implement <code>experiment()</code> first!")
return redirect(url_for('experiment', exp=exp))
go_list = [es.go_aspect(a) for a in aspect]
if None in go_list:
flash("You need to implement <code>go_aspect()</code> first!")
return redirect(url_for('experiment', exp=exp))
go_list = list(reduce(set.union, go_list, set()))
go_info = {goid:es.go_info(goid) for goid in go_list}
go_dict = {gene:es.go_to_gene(gene) for gene in go_list}
scores = hs.calculate_enrichment(exp_data, go_dict, n)
return render_template("enrichment.html", exp=exp, go_info=go_info,
e_scores=scores[0][:10], ne_scores=scores[1][:10])
def enrichment(exp, aspect, n=100):
aspect = set(aspect)
if not aspect.intersection('CFP'):
flash("That's not a valid aspect, try C, F, and/or P")
return redirect(url_for('experiment', exp=exp))
exp_data = es.experiment()
if exp_data is not None:
exp_data = exp_data[exp]
else:
flash("You need to implement <code>experiment()</code> first!")
return redirect(url_for('experiment', exp=exp))
go_list = list(reduce(set.union, (es.go_aspect(a) for a in aspect), set()))
go_info = {goid:es.go_info(goid) for goid in go_list}
go_dict = {gene:es.go_to_gene(gene) for gene in go_list}
scores = hs.calculate_enrichment(exp_data, go_dict, n)
return render_template("enrichment.html", exp=exp, go_info=go_info,
e_scores=scores[0][:10], ne_scores=scores[1][:10])
