def region_page(chrom, start, stop):
db = get_db()
try:
_log()
try:
start = int(start)
except:
return bad_request_page('The start position {!s} is not integer.'.format(start))
try:
stop = int(stop)
except:
return bad_request_page('The stop position {!s} is not integer.'.format(stop))
if start > stop:
return bad_request_page("The region '{chrom}-{start}-{stop}' stops before it starts. Did you mean '{chrom}-{stop}-{start}'?".format(chrom = chrom, start = start, stop = stop))
if stop-start > MAX_REGION_LENGTH:
return bad_request_page("The region '{chrom}-{start}-{stop}' is {:,} bases. We only accept regions shorter than {:,} bases.".format(stop - start, MAX_REGION_LENGTH, chrom = chrom, start = start, stop = stop))
if start == stop:
start -= 20
stop += 20
intervalset = IntervalSet.from_chrom_start_stop(chrom, start, stop)
genes = TranscriptSet.from_chrom_start_stop(db, chrom, start, stop).genes
return render_template(
'region.html',
intervalset = intervalset, genes = genes, csq = Consequence.as_obj,
)
except: _err(); abort(500)
def region_variants_subset_api(chrom, start, stop):
try:
start, stop = int(start), int(stop)
assert stop - start <= MAX_REGION_LENGTH
intervalset = IntervalSet.from_chrom_start_stop(chrom, start, stop)
return _get_variants_subset_response_for_intervalset(intervalset)
except:
_err()
abort(500)
def region_coverage_api(chrom, start, stop):
try:
start, stop = int(start), int(stop)
assert stop - start <= MAX_REGION_LENGTH
intervalset = IntervalSet.from_chrom_start_stop(chrom, start, stop)
return jsonify(
get_coverage_handler().get_coverage_for_intervalset(intervalset))
except:
_err()
abort(500)
def region_summary_api(chrom, start, stop):
try:
start, stop = int(start), int(stop)
assert stop - start <= MAX_REGION_LENGTH
intervalset = IntervalSet.from_chrom_start_stop(chrom, start, stop)
return jsonify(
lookups.get_summary_for_intervalset(get_db(), intervalset))
except:
_err()
abort(500)
def download_region_variants(chrom, start, stop):
try:
start, stop = int(start), int(stop)
assert stop - start <= MAX_REGION_LENGTH
intervalset = IntervalSet.from_chrom_start_stop(chrom, start, stop)
return _get_variants_csv_for_intervalset(
intervalset, 'chr{}-{}-{}.csv'.format(chrom, start, stop))
except:
_err()
abort(500)