def genotype_details(genotype_id):
"""
Flask function to return genotype info, dashboard, etc.
"""
var_mgr = variant_manager(db="test",conn=g.conn)
data = var_mgr.get_variant(genotype_id)
if "EFF" in data["annotations"]:
for ix, row in enumerate(data["annotations"]["EFF"]):
data["annotations"]["EFF"][ix]["effect_code"] = VARIANT_EFFECTS[row["e"]]
data["dashboard"] = {}
data["dashboard"]["gatk"] = []
data["dashboard"]["gatk"].append({"title": "QUAL", "score": data["qual"]})
#data["dashboard"]["gatk"].append({"title": "DATA", "score": data["data"]})
data["dashboard"]["gatk"].append({"title": "FILTER", "score": "GATK_filter" in data["filter"]})
for name, value in data["annotations"].items():
if name in ["MQ", "DP", "AB"]:
data["dashboard"]["gatk"].append({"title": name, "score": value})
if "dbNSFP" in data["annotations"]:
data["dashboard"]["scores"] = []
for score_name, score_value in data["annotations"]["dbNSFP"].items():
print score_name, score_value
data["dashboard"]["scores"].append({"title":score_name, "score": score_value})
data["dashboard"]["freq"] = [{"title": "ESP",
"freqs": [{"pop":"AA", "freq": round(data["annotations"]["dbNSFP"].get("ESPaa", 0),3)},
{"pop":"EA", "freq": round(data["annotations"]["dbNSFP"].get("ESPea", 0),3)}]},
{"title": "1KG", "overallfreq": data["annotations"]["dbNSFP"].get("1gALLac", 0),
"freqs": [{"pop":"AFR", "freq": data["annotations"]["dbNSFP"].get("1gAFRac",0)},
{"pop":"EUR", "freq": data["annotations"]["dbNSFP"].get("1gEURac",0)},
{"pop":"ASN", "freq": data["annotations"]["dbNSFP"].get("1gASNac",0)},
{"pop":"AMR", "freq": data["annotations"]["dbNSFP"].get("1gAMRac",0)}]}]
return render_template("genotype_details.html", data=data)
def variants():
"""
Flask function for variants home page. Various stats on the
database are returned, not much else. A search box is provided
as well.
"""
var_mgr = variant_manager(db="test",conn=g.conn)
stats = var_mgr.get_db_stats()
return render_template("variants.html", stats=stats)
def variant_details(chrom, start, end=None):
"""
Flask function to render the variant-level (not genotype) details
Currently returns list of samples with this genotype.
"""
var_mgr = variant_manager(db="test",conn=g.conn)
if end is None:
genotype_data = var_mgr.get_variants_by_position(chrom, start)
else:
genotype_data = var_mgr.get_variants_by_position(chrom, start, end)
variant_data = var_mgr.get_variant(genotype_data[0]["_id"])
for ix, row in enumerate(variant_data["annotations"]["EFF"]):
variant_data["annotations"]["EFF"][ix]["effect_code"] = VARIANT_EFFECTS[row["e"]]
return render_template("variant_details.html", variant_data=variant_data, genotype_data=genotype_data)
def __init__(self, db, conn):
super(GaussQuery, self).__init__()
self.db = db
self.conn = conn
self.var_mgr = variant_manager(db=self.db, conn=self.conn)
self.filter_mgr = filter_manager(db=self.db, conn=self.conn)
self.column_list = ["chrom", "start", "end", "sample_name", "id", "ref", "alt"]
self.custom_column_list = []
self.projection = {k: True for k in self.column_list}
#del self.projection["end"] # may not be necessary
self.projection["filter"] = True # can add to column_list?
self.projection["annotations.EFF"] = True # can add to column list?
self.grouped = False
self.skip = 0
self.limit = 1000
self.query = defaultdict(lambda: defaultdict(list))
def samples_info(sample_id):
"""
Flask function to return sample info page. Returns a summary of
the number of variants in this sample, as well as the files attached
to this sample and metadata.
"""
mgr = sample_manager(db="test",conn=g.conn)
var_mgr = variant_manager(db="test",conn=g.conn)
data = mgr.get_sample(sample_id = sample_id)
effect_summary = var_mgr.get_sample_variant_summary(data["_id"])
for row in effect_summary:
eff_code = row["_id"]
eff_type = VARIANT_EFFECTS[eff_code]
eff_rank = VARIANT_RANKS[eff_type]
row["effect_str"] = Markup("<span class='label impact-tag %s'>%s</span>" % (eff_type, VARIANT_SHORTNAMES[eff_code]))
row["effect_rank"] = eff_rank
rank_sort = np.argsort(map(operator.itemgetter("effect_rank"), effect_summary))
data["variant_summary"] = [effect_summary[i] for i in rank_sort[::-1]]
return render_template("sample_info.html", sample_id=sample_id, info=data)