def gene(gene_name):
title = gene_name
tbl_color = {"LOW": 'success', "MODERATE": 'warning', "HIGH": 'danger'}
bcs = OrderedDict([("Gene", None), (title, None)])
result = list(wb_gene.filter((wb_gene.Name == gene_name) |
(wb_gene.sequence_name == gene_name) |
(wb_gene.locus == gene_name)).dicts().execute())
if len(result) != 1:
return render_template('404.html'), 404
gene_record = result[0]
# Retrieve variants
variants = WI.select().filter(
WI.CHROM == gene_record["CHROM"],
WI.gene_id == gene_record["Name"]).dicts().execute()
# Retrieve mappings
mapping_set = mapping.select(mapping, trait, report) \
.join(trait) \
.join(report) \
.where((gene_record["CHROM"] == mapping.chrom) &
(report.release == 0) &
(gene_record["start"] >= mapping.interval_start) &
(gene_record["end"] <= mapping.interval_end)) \
.dicts() \
.execute()
return render_template('gene.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 trait_view(report_slug, trait_slug="", rerun=None):
report_data = list(
report.select(report, trait, mapping.trait_id)
.join(trait)
.where(
((report.report_slug == report_slug) & (report.release == 0))
| ((report.report_hash == report_slug) & (report.release > 0))
)
.join(mapping, JOIN.LEFT_OUTER)
.distinct()
.dicts()
.execute()
)
if not report_data:
return render_template("404.html"), 404
if report_data[0]["release"] == 0:
report_url_slug = report_data[0]["report_slug"]
else:
report_url_slug = report_data[0]["report_hash"]
if not trait_slug:
return redirect(url_for("trait_view", report_slug=report_url_slug, trait_slug=report_data[0]["trait_slug"]))
else:
try:
trait_data = [x for x in report_data if x["trait_slug"] == trait_slug][0]
except:
# Redirect user to first trait if it can't be found.
return redirect(url_for("trait_view", report_slug=report_url_slug, trait_slug=report_data[0]["trait_slug"]))
page_title = trait_data["report_name"] + " > " + trait_data["trait_name"]
title = trait_data["report_name"]
subtitle = trait_data["trait_name"]
# Define report and trait slug
report_slug = trait_data["report_slug"] # don't remove
trait_slug = trait_data["trait_slug"] # don't remove
r = report.get(report_slug=report_slug)
t = trait.get(report=r, trait_slug=trait_slug)
# phenotype data
phenotype_data = list(
trait_value.select(strain.strain, trait_value.value)
.join(trait)
.join(report)
.switch(trait_value)
.join(strain)
.where(report.report_slug == r.report_slug)
.where(trait.trait_slug == t.trait_slug)
.dicts()
.execute()
)
if rerun == "rerun":
t.status = "queue"
t.save()
launch_mapping(verify_request=False)
# Return user to current trait
return redirect(url_for("trait_view", report_slug=report_url_slug, trait_slug=trait_slug))
report_trait = "%s/%s" % (report_slug, trait_slug)
base_url = "https://storage.googleapis.com/cendr/" + report_trait
# Fetch significant mappings
mapping_results = list(
mapping.select(mapping, report, trait)
.join(trait)
.join(report)
.filter((report.report_slug == report_slug), (trait.trait_slug == trait_slug))
.dicts()
.execute()
)
#######################
# Variant Correlation #
#######################
var_corr = []
for m in mapping_results:
var_corr.append(correlation.get_correlated_genes(r, t, m["chrom"], m["interval_start"], m["interval_end"]))
tbl_color = {"LOW": "success", "MODERATE": "warning", "HIGH": "danger"}
#######################
# Fetch geo locations #
#######################
geo_gt = {}
for m in mapping_results:
try:
result = GT.fetch_geo_gt(m["chrom"], m["pos"])
geo_gt[m["chrom"] + ":" + str(m["pos"])] = result
except:
pass
geo_gt = json.dumps(geo_gt)
status = trait_data["status"]
# List available datasets
report_files = list(storage.Client().get_bucket("cendr").list_blobs(prefix=report_trait + "/tables"))
report_files = [os.path.split(x.name)[1] for x in report_files]
# Fetch biotypes descriptions
from cendr import biotypes
return render_template("report.html", **locals())
def public_mapping():
query = request.args.get("query")
if query is not None:
bcs = OrderedDict([("Public Mappings", url_for("public_mapping")), ("Search", None)])
title = "Search: " + query
subtitle = "results"
q = "%" + query + "%"
results = (
trait.select(report, trait, mapping)
.filter(trait.status == "complete", report.release == 0)
.join(mapping)
.join(report)
.dicts()
.filter(
(trait.trait_slug % q) | (trait.trait_name % q) | (report.report_name % q) | (report.report_slug % q)
)
.order_by(mapping.log10p.desc())
)
search_results = list(results.dicts().execute())
search = True
return render_template("public_mapping.html", **locals())
title = "Perform Mapping"
results = (
trait.select(
report.release,
report.report_name,
report.report_slug,
trait.trait_name,
trait.trait_slug,
trait.status,
trait.submission_complete,
trait.submission_date,
mapping,
)
.filter(trait.status == "complete", report.release == 0)
.join(mapping, JOIN.LEFT_OUTER)
.switch(trait)
.join(report)
.distinct()
.dicts()
.order_by(trait.submission_complete.desc())
.execute()
)
date_set = dict(
Counter([time.mktime((x["submission_date"] + relativedelta(hours=+6)).timetuple()) for x in results])
)
wdata = Counter([(x["submission_date"] + relativedelta(hours=+6)).date().isoformat() for x in results])
waffle_date_set = [{"date": x, "count": y} for x, y in wdata.items()]
# added in here waffle_date_set should be filtered by month instead of time stamp. Then could be used for the waffle plot
# submission date is a datetime object
# waffle_date_set=[]
# sum=0
# current_month=results[0]["submission_date"].month
# for x in results:
# if x["submission_date"].month==current_month:
# sum++
# else:
# waffle_date_set.append(("month": current_month, "total": sum)) #appending a tuple
# sum=1
# current_month=x["submission_date"].month
recent_results = list(results)[0:20]
bcs = OrderedDict([("Public", None)])
title = "Public Mappings"
pub_mappings = list(
mapping.select(mapping, report, trait).join(trait).join(report).filter(report.release == 0).dicts().execute()
)
return render_template("public_mapping.html", **locals())