def view(organism, symbol):
# if we came from the search page then we know the symbol has been
# found already, othwerise was entered in the URL so do search
if not request.referrer or not request.referrer.endswith('search'):
genes = pd.find_gene(symbol, org_util.get_name(organism))
if len(genes) == 1:
symbol = genes[0][0]
else:
flash('Could not find gene: ' + symbol + ' in organism ' + organism)
return redirect(url_for('search'))
org_full_name = org_util.get_name(organism)
homologs = pd.get_homologs_for_gene(symbol, org_full_name)
# include starting gene in search
all_orgs = dict(homologs)
if not org_full_name in all_orgs:
all_orgs[org_full_name] = {}
all_orgs[org_full_name][symbol] = None
# fetch pathways
pathways = []
for org in all_orgs:
for gene in all_orgs[org]:
for pws in pd.get_pathways(gene, org):
pathways.append(pws)
# re-organise for display: {pathway: {organisms: [genes]}}
table = defaultdict(lambda: defaultdict(list))
for row in pathways:
table[row[0]][row[1]].append(row[2])
return render_template('view.html', symbol=symbol, organism=org_full_name, org_abbrev=organism, orgs=all_orgs, homologs=homologs, table=table)
def view(organism, symbol):
# if we came from the search page then we know the symbol has been
# found already, othwerise was entered in the URL so do search
if not request.referrer or not request.referrer.endswith('search'):
genes = pd.find_gene(symbol, org_util.get_name(organism))
if len(genes) == 1:
symbol = genes[0][0]
else:
flash('Could not find gene: ' + symbol + ' in organism ' +
organism)
return redirect(url_for('search'))
org_full_name = org_util.get_name(organism)
homologs = pd.get_homologs_for_gene(symbol, org_full_name)
# include starting gene in search
all_orgs = dict(homologs)
if not org_full_name in all_orgs:
all_orgs[org_full_name] = {}
all_orgs[org_full_name][symbol] = None
# fetch pathways
pathways = []
for org in all_orgs:
for gene in all_orgs[org]:
for gene_pathways in pd.get_pathways(gene, org):
pathways.append(gene_pathways)
# re-organise for display: {pathway: {organisms: [genes]}}
table = defaultdict(lambda: defaultdict(list))
for row in pathways:
table[row[0]][row[1]].append(row[2])
return render_template('view.html',
symbol=symbol,
organism=org_full_name,
org_abbrev=organism,
orgs=all_orgs,
homologs=homologs,
table=table)
def search():
if request.method == 'POST':
symbol = request.form['symbol']
org = request.form['organism']
if symbol:
genes = pd.find_gene(symbol, org_util.get_name(org))
if len(genes) == 1:
symbol = genes[0][0]
return redirect(url_for('view', symbol=symbol, organism=org))
flash('Could not find gene: ' + symbol + ' in organism ' + org)
return redirect(url_for('search'))
else:
orgs = org_util.get_abbrevs()
return render_template('search.html', organisms=orgs)
def search():
if request.method == 'POST':
symbol = request.form['symbol']
org = request.form['organism']
if symbol:
genes = pd.find_gene(symbol, org_util.get_name(org))
if len(genes) == 1:
symbol = genes[0][0]
return redirect(url_for('view', symbol=symbol, organism=org))
flash('Could not find gene: ' + symbol + ' in organism ' + org)
return redirect(url_for('search'))
else:
orgs = org_util.get_abbrevs()
return render_template('search.html', organisms=orgs)
