def data_page():
bcs = OrderedDict([("Data", None)])
title = "Data"
from cendr import build
strain_listing = strain.select().filter(
strain.isotype != None).order_by(strain.isotype).execute()
return render_template('data.html', **locals())
def statistics():
title = "Site Statistics"
bcs = OrderedDict([("About", url_for("about")), ("Statistics", None)])
# Number of reports
n_reports = report.select().count()
n_traits = trait.select().count()
n_significant_mappings = mapping.select().count()
n_distinct_strains = strain.select(strain.strain).distinct().count()
n_distinct_isotypes = strain.select(strain.isotype).filter(strain.isotype != None).distinct().count()
# Collection dates
collection_dates = list(strain.select().filter(
strain.isotype != None, strain.isolation_date != None).order_by(strain.isolation_date).execute())
return render_template('statistics.html', **locals())
def download_script(filetype):
strain_listing = strain.select().filter(
strain.isotype != None).order_by(strain.isotype).execute()
download_page = render_template('download_script.sh', **locals())
response = make_response(download_page)
response.headers["Content-Type"] = "text/plain"
return response
def about():
# About us Page - directs to other pages.
title = "About"
bcs = OrderedDict([("About", None)])
strain_listing = list(strain.select().filter(strain.isotype.is_null() == False)
.filter(strain.latitude.is_null() == False).execute())
strain_listing = json.dumps([x.__dict__["_data"] for x in strain_listing], default=json_serial)
return render_template('about.html', **locals())
def map_page():
title = "Global Strain Map"
bcs = OrderedDict([("Strain", url_for("strain_listing_page")), ("Global-Strain-Map", "")])
strain_list_dicts = []
strain_listing = list(strain.select().filter(strain.reference_strain == True)
.filter(strain.latitude.is_null() == False).execute())
strain_listing = json.dumps([x.__dict__["_data"] for x in strain_listing], default=json_serial)
return render_template('map.html', **locals())
def get(self, isotype_name):
"""
Return all strains within an isotype.
"""
strain_data = list(strain.select(
strain.strain).filter(strain.isotype == isotype_name).execute())
response = [x.strain for x in strain_data]
return jsonify(response)
def get(self):
"""
Return information for all strains.
"""
strain_data = list(strain.select(
*PEEWEE_FIELDS_LIST).tuples().execute())
response = [OrderedDict(zip(FIELDS, x)) for x in strain_data]
return jsonify(response)
def get(self, strain_name):
"""
Return information for an individual strain.
"""
strain_data = list(strain.select(
*PEEWEE_FIELDS_LIST).filter(strain.strain == strain_name)
.tuples()
.execute())
response = OrderedDict(zip(FIELDS, strain_data[0]))
print response, "RESPONSE"
return jsonify(response)
def strain_metadata():
strain_listing = list(strain.select().filter(
strain.isotype != None).tuples().execute())
def generate():
yield '\t'.join(strain._meta.sorted_field_names[1:21]) + "\n"
for row in strain_listing:
row = list(row)
for k, f in enumerate(row):
if type(f) == unicode:
row[k] = f.encode('ascii', 'ignore')
yield '\t'.join(map(str, row[1:21])) + "\n"
return Response(generate(), mimetype="text/tab-separated-values")
def browser(chrom = "III", start = 11746923, end = 11750250, tracks="mh"):
bcs = OrderedDict([("Data", "/data"), ("Browser", None)])
title = "Browser"
putative_impact = {'l': 'LOW', 'm':'MODERATE', 'h': 'HIGH'}
var_eff = [putative_impact[x] if x else '' for x in tracks]
putative_impact_items = putative_impact.items()
from cendr import build
isotype_listing = list(strain.select(strain.isotype).distinct().filter(
strain.isotype != None).order_by(strain.isotype).dicts().execute())
isotypes = [x["isotype"] for x in isotype_listing]
return render_template('browser.html', **locals())
def strain_listing_page():
bcs = OrderedDict([("Strain", None)])
title = "Strain Catalog"
if 'warning' in request.args:
warning = request.args["warning"]
strain_listing = strain.select(strain.strain,
strain.reference_strain,
strain.isotype,
strain.previous_names,
strain.set_1,
strain.set_2,
strain.set_3,
strain.set_4,
strain.set_divergent).filter(strain.isotype != None).order_by(strain.isotype).execute()
return render_template('strain_catalog.html', **locals())
def gwa():
title = "Perform Mapping"
bcs = OrderedDict([("Perform-Mapping", None)])
# Generate list of allowable strains
query = (
strain.select(strain.strain, strain.isotype, strain.previous_names)
.filter(strain.isotype.is_null() == False)
.execute()
)
qresults = list(itertools.chain(*[[x.strain, x.isotype, x.previous_names] for x in query]))
qresults = set([x for x in qresults if x != None])
qresults = list(itertools.chain(*[x.split("|") for x in qresults]))
embargo_release = (datetime.now(pytz.timezone("America/Chicago")) + relativedelta(years=1)).strftime("%m/%d/%Y")
strain_list = json.dumps(qresults)
return render_template("gwa.html", **locals())
def fetch_geo_gt(chrom, pos):
"""
Fetch genotypes with strain geographic information
"""
gt = get_gt(chrom, pos)
strain_locations = list(strain.select(strain.isotype,
strain.latitude,
strain.longitude)
.filter(strain.latitude != None)
.distinct().dicts().execute())
strain_locations = {x["isotype"]: x for x in strain_locations}
for i in gt:
if i["SAMPLE"] in strain_locations and i["GT"] in ["0/0", "1/1"]:
gts = {"TGT": i["TGT"], "GT": i["GT"]}
strain_locations[i["SAMPLE"]].update(gts)
else:
if i["SAMPLE"] in strain_locations:
del strain_locations[i["SAMPLE"]]
return strain_locations.values()
