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])