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 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 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 gene_info(gene):
gene_name = es.gene_name(gene)
gene_info = es.gene_info(gene)
if gene_name is None or gene_info is None:
if gene_name is None:
flash("You need to implement <code>gene_name()</code>")
if gene_info is None:
flash("You need to implement <code>gene_info()</code>")
return redirect(url_for('homepage'))
go_terms = es.gene_to_go(gene)
go_terms = [(goid, es.go_info(goid)) for goid in go_terms]
return render_template("gene.html", gene_name=gene_name,
gene_info=gene_info, go_terms=go_terms)
def gene_info(gene=None):
if gene is None:
flash("That page needs a gene ID")
return redirect(url_for("homepage"))
gene_name = es.gene_name(gene)
gene_info = es.gene_info(gene)
if gene_name is None or gene_info is None:
if gene_name is None:
flash("You need to implement <code>gene_name()</code>")
if gene_info is None:
flash("You need to implement <code>gene_info()</code>")
return redirect(url_for('homepage'))
go_terms = es.gene_to_go(gene)
if go_terms is None:
flash("You need to implement <code>gene_to_go()</code>")
go_terms = []
else:
go_terms = [(goid, es.go_info(goid)) for goid in go_terms]
if go_terms and go_terms[0][1] is None:
flash("You need to implement <code>go_info()</code>")
gene_data = es.gene_data(gene)
if gene_data is None:
flash("You need to implement <code>gene_data()</code>")
hist_data = None
else:
gene_hist,bins = np.histogram(gene_data, bins=np.linspace(-8, 8, 33))
hist_data = zip(bins[:-1], gene_hist)
local_network = hs.go_network(gene, False, 2)
if local_network is None:
flash("You should 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("gene.html", gene_name=gene_name,
gene_info=gene_info, go_terms=go_terms,
hist_data=hist_data, local_network=local_network)
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])
