def region_page(region_id):
dbname = session['db_selected']
db = get_db()
try:
region = region_id.split('-')
cache_key = 't-region-{}'.format(region_id)
t = cache.get(cache_key)
print 'Rendering %sregion: %s' % ('' if t is None else 'cached ',
region_id)
if t is None:
chrom = region[0]
start = None
stop = None
if len(region) == 3:
chrom, start, stop = region
start = int(start)
stop = int(stop)
if start is None or stop - start > REGION_LIMIT or stop < start:
return render_template(
'region.html',
genes_in_region=None,
variants_in_region=None,
chrom=chrom,
start=start,
stop=stop,
coverage=None,
csq_order=csq_order,
dbname=dbname,
)
if start == stop:
start -= 20
stop += 20
genes_in_region = lookups.get_genes_in_region(
db, chrom, start, stop)
variants_in_region = lookups.get_variants_in_region(
db, chrom, start, stop)
xstart = get_xpos(chrom, start)
xstop = get_xpos(chrom, stop)
coverage_array = lookups.get_coverage_for_bases(db, xstart, xstop)
t = render_template(
'region.html',
genes_in_region=genes_in_region,
variants_in_region=variants_in_region,
chrom=chrom,
start=start,
stop=stop,
coverage=coverage_array,
csq_order=csq_order,
dbname=dbname,
)
cache.set(cache_key, t)
return t
except Exception, e:
print 'Failed on region:', region_id, ';Error=', traceback.format_exc()
abort(404)
def region_page(region_id):
db = get_db()
try:
region = region_id.split('-')
cache_key = 't-region-{}'.format(region_id)
t = cache.get(cache_key)
if t is None:
chrom = region[0]
start = None
stop = None
if len(region) == 3:
chrom, start, stop = region
start = int(start)
stop = int(stop)
if start is None or stop - start > REGION_LIMIT or stop < start:
return render_template(
'region.html',
genes_in_region=None,
variants_in_region=None,
chrom=chrom,
start=start,
stop=stop,
coverage=None
)
if start == stop:
start -= 20
stop += 20
genes_in_region = lookups.get_genes_in_region(db, chrom, start, stop)
variants_in_region = lookups.get_variants_in_region(db, chrom, start, stop)
xstart = get_xpos(chrom, start)
xstop = get_xpos(chrom, stop)
coverage_stats_exomes = lookups.get_coverage_for_bases(db, 'exome_coverage', xstart, xstop)
coverage_stats_genomes = lookups.get_coverage_for_bases(db, 'genome_coverage', xstart, xstop)
coverage_stats = {
"exomes": coverage_stats_exomes,
"genomes": coverage_stats_genomes
}
t = render_template(
'region.html',
genes_in_region=genes_in_region,
variants_in_region=variants_in_region,
chrom=chrom,
start=start,
stop=stop,
coverage=coverage_stats
)
print 'Rendering region: %s' % region_id
return t
except Exception, e:
print 'Failed on region:', region_id, ';Error=', traceback.format_exc()
abort(404)
def region_page(region_id):
db = get_db()
try:
region = region_id.split('-')
cache_key = 't-region-{}'.format(region_id)
t = cache.get(cache_key)
print 'Rendering %sregion: %s' % ('' if t is None else 'cached ', region_id)
if t is None:
chrom = region[0]
start = None
stop = None
if len(region) == 3:
chrom, start, stop = region
start = int(start)
stop = int(stop)
if start is None or stop - start > REGION_LIMIT or stop < start:
return render_template(
'region.html',
genes_in_region=None,
variants_in_region=None,
chrom=chrom,
start=start,
stop=stop,
coverage=None,
csq_order=csq_order,
)
if start == stop:
start -= 20
stop += 20
genes_in_region = lookups.get_genes_in_region(db, chrom, start, stop)
variants_in_region = lookups.get_variants_in_region(db, chrom, start, stop)
xstart = get_xpos(chrom, start)
xstop = get_xpos(chrom, stop)
coverage_array = lookups.get_coverage_for_bases(db, xstart, xstop)
t = render_template(
'region.html',
genes_in_region=genes_in_region,
variants_in_region=variants_in_region,
chrom=chrom,
start=start,
stop=stop,
coverage=coverage_array,
csq_order=csq_order,
)
cache.set(cache_key, t)
return t
except Exception, e:
print 'Failed on region:', region_id, ';Error=', traceback.format_exc()
abort(404)
def region_page(region_id):
db = get_db()
try:
region = region_id.split("-")
cache_key = "t-region-{}".format(region_id)
t = cache.get(cache_key)
if t is None:
chrom = region[0]
start = None
stop = None
if len(region) == 3:
chrom, start, stop = region
start = int(start)
stop = int(stop)
if start is None or stop - start > REGION_LIMIT or stop < start:
return render_template(
"region.html",
genes_in_region=None,
variants_in_region=None,
chrom=chrom,
start=start,
stop=stop,
coverage=None,
)
if start == stop:
start -= 20
stop += 20
genes_in_region = lookups.get_genes_in_region(db, chrom, start, stop)
variants_in_region = lookups.get_variants_in_region(db, chrom, start, stop)
xstart = get_xpos(chrom, start)
xstop = get_xpos(chrom, stop)
coverage_array = lookups.get_coverage_for_bases(db, xstart, xstop)
t = render_template(
"region.html",
genes_in_region=genes_in_region,
variants_in_region=variants_in_region,
chrom=chrom,
start=start,
stop=stop,
coverage=coverage_array,
)
print "Rendering region: %s" % region_id
return t
except Exception, e:
print "Failed on region:", region_id, ";Error=", e
abort(404)
def region_page(region_id):
db = get_db()
try:
region = region_id.split('-')
cache_key = 't-region-{}'.format(region_id)
t = cache.get(cache_key)
if t is None:
chrom = region[0]
start = None
stop = None
if len(region) == 3:
chrom, start, stop = region
start = int(start)
stop = int(stop)
if start is None or stop - start > REGION_LIMIT:
return render_template(
'region.html',
genes_in_region=None,
variants_in_region=None,
chrom=chrom,
start=start,
stop=stop,
coverage=None
)
genes_in_region = lookups.get_genes_in_region(db, chrom, start, stop)
variants_in_region = lookups.get_variants_in_region(db, chrom, start, stop)
xstart = xbrowse.get_xpos(chrom, start)
xstop = xbrowse.get_xpos(chrom, stop)
coverage_array = lookups.get_coverage_for_bases(db, xstart, xstop)
t = render_template(
'region.html',
genes_in_region=genes_in_region,
variants_in_region=variants_in_region,
chrom=chrom,
start=start,
stop=stop,
coverage=coverage_array
)
print 'Rendering region: %s' % region_id
return t
except Exception, e:
print 'Failed on region:', region_id, ';Error=', e
abort(404)
def region_page(region_id):
db = get_db()
try:
region = region_id.split('-')
cache_key = 't-region-{}'.format(region_id)
t = cache.get(cache_key)
if t is None:
chrom = region[0]
start = None
stop = None
if len(region) == 3:
chrom, start, stop = region
start = int(start)
stop = int(stop)
if start is None or stop - start > REGION_LIMIT:
return render_template('region.html',
genes_in_region=None,
variants_in_region=None,
chrom=chrom,
start=start,
stop=stop,
coverage=None)
genes_in_region = lookups.get_genes_in_region(
db, chrom, start, stop)
variants_in_region = lookups.get_variants_in_region(
db, chrom, start, stop)
xstart = xbrowse.get_xpos(chrom, start)
xstop = xbrowse.get_xpos(chrom, stop)
coverage_array = lookups.get_coverage_for_bases(db, xstart, xstop)
t = render_template('region.html',
genes_in_region=genes_in_region,
variants_in_region=variants_in_region,
chrom=chrom,
start=start,
stop=stop,
coverage=coverage_array)
print 'Rendering region: %s' % region_id
return t
except Exception, e:
print 'Failed on region:', region_id, ';Error=', e
abort(404)