def transcript_page(transcript_id):
db = get_db()
try:
transcript = lookups.get_transcript(db, transcript_id)
cache_key = 't-transcript-{}'.format(transcript_id)
t = cache.get(cache_key)
if t is None:
gene = lookups.get_gene(db, transcript['gene_id'])
gene['transcripts'] = lookups.get_transcripts_in_gene(
db, transcript['gene_id'])
variants_in_transcript = lookups.get_variants_in_transcript(
db, transcript_id)
cnvs_in_transcript = lookups.get_exons_cnvs(db, transcript_id)
cnvs_per_gene = lookups.get_cnvs(db, transcript['gene_id'])
coverage_stats = lookups.get_coverage_for_transcript(
db, transcript['xstart'] - EXON_PADDING,
transcript['xstop'] + EXON_PADDING)
add_transcript_coordinate_to_variants(db, variants_in_transcript,
transcript_id)
t = render_template(
'transcript.html',
transcript=transcript,
transcript_json=json.dumps(transcript),
variants_in_transcript=variants_in_transcript,
variants_in_transcript_json=json.dumps(variants_in_transcript),
coverage_stats=coverage_stats,
coverage_stats_json=json.dumps(coverage_stats),
gene=gene,
gene_json=json.dumps(gene),
cnvs=cnvs_in_transcript,
cnvs_json=json.dumps(cnvs_in_transcript),
cnvgenes=cnvs_per_gene,
cnvgenes_json=json.dumps(cnvs_per_gene))
cache.set(cache_key, t, timeout=1000 * 60)
print 'Rendering transcript: %s' % transcript_id
return t
except Exception, e:
print 'Failed on transcript:', transcript_id, ';Error=', traceback.format_exc(
)
abort(404)
def get_gene_page_content(gene_id):
db = get_db()
try:
gene = lookups.get_gene(db, gene_id)
if gene is None:
abort(404)
cache_key = 't-gene-{}'.format(gene_id)
t = cache.get(cache_key)
if t is None:
variants_in_gene = lookups.get_variants_in_gene(db, gene_id)
transcripts_in_gene = lookups.get_transcripts_in_gene(db, gene_id)
# Get some canonical transcript and corresponding info
transcript_id = gene['canonical_transcript']
transcript = lookups.get_transcript(db, transcript_id)
variants_in_transcript = lookups.get_variants_in_transcript(
db, transcript_id)
cnvs_in_transcript = lookups.get_exons_cnvs(db, transcript_id)
cnvs_per_gene = lookups.get_cnvs(db, gene_id)
coverage_stats = lookups.get_coverage_for_transcript(
db, transcript['xstart'] - EXON_PADDING,
transcript['xstop'] + EXON_PADDING)
add_transcript_coordinate_to_variants(db, variants_in_transcript,
transcript_id)
constraint_info = lookups.get_constraint_for_transcript(
db, transcript_id)
t = render_template('gene.html',
gene=gene,
transcript=transcript,
variants_in_gene=variants_in_gene,
variants_in_transcript=variants_in_transcript,
transcripts_in_gene=transcripts_in_gene,
coverage_stats=coverage_stats,
cnvs=cnvs_in_transcript,
cnvgenes=cnvs_per_gene,
constraint=constraint_info)
cache.set(cache_key, t, timeout=1000 * 60)
print 'Rendering gene: %s' % gene_id
return t
except Exception, e:
print 'Failed on gene:', gene_id, ';Error=', traceback.format_exc()
abort(404)
def get_gene_page_content(gene_id):
db = get_db()
try:
gene = lookups.get_gene(db, gene_id)
if gene is None:
abort(404)
cache_key = 't-gene-{}'.format(gene_id)
t = cache.get(cache_key)
if t is None:
variants_in_gene = lookups.get_variants_in_gene(db, gene_id)
transcripts_in_gene = lookups.get_transcripts_in_gene(db, gene_id)
# Get some canonical transcript and corresponding info
transcript_id = gene['canonical_transcript']
transcript = lookups.get_transcript(db, transcript_id)
variants_in_transcript = lookups.get_variants_in_transcript(db, transcript_id)
cnvs_in_transcript = lookups.get_exons_cnvs(db, transcript_id)
cnvs_per_gene = lookups.get_cnvs(db, gene_id)
coverage_stats = lookups.get_coverage_for_transcript(db, transcript['xstart'] - EXON_PADDING, transcript['xstop'] + EXON_PADDING)
add_transcript_coordinate_to_variants(db, variants_in_transcript, transcript_id)
constraint_info = lookups.get_constraint_for_transcript(db, transcript_id)
t = render_template(
'gene.html',
gene=gene,
transcript=transcript,
variants_in_gene=variants_in_gene,
variants_in_transcript=variants_in_transcript,
transcripts_in_gene=transcripts_in_gene,
coverage_stats=coverage_stats,
cnvs = cnvs_in_transcript,
cnvgenes = cnvs_per_gene,
constraint=constraint_info
)
cache.set(cache_key, t, timeout=1000*60)
print 'Rendering gene: %s' % gene_id
return t
except Exception, e:
print 'Failed on gene:', gene_id, ';Error=', traceback.format_exc()
abort(404)
def transcript_page(transcript_id):
db = get_db()
try:
transcript = lookups.get_transcript(db, transcript_id)
cache_key = 't-transcript-{}'.format(transcript_id)
t = cache.get(cache_key)
if t is None:
gene = lookups.get_gene(db, transcript['gene_id'])
gene['transcripts'] = lookups.get_transcripts_in_gene(db, transcript['gene_id'])
variants_in_transcript = lookups.get_variants_in_transcript(db, transcript_id)
cnvs_in_transcript = lookups.get_exons_cnvs(db, transcript_id)
cnvs_per_gene = lookups.get_cnvs(db, transcript['gene_id'])
coverage_stats = lookups.get_coverage_for_transcript(db, transcript['xstart'] - EXON_PADDING, transcript['xstop'] + EXON_PADDING)
add_transcript_coordinate_to_variants(db, variants_in_transcript, transcript_id)
t = render_template(
'transcript.html',
transcript=transcript,
transcript_json=json.dumps(transcript),
variants_in_transcript=variants_in_transcript,
variants_in_transcript_json=json.dumps(variants_in_transcript),
coverage_stats=coverage_stats,
coverage_stats_json=json.dumps(coverage_stats),
gene=gene,
gene_json=json.dumps(gene),
cnvs = cnvs_in_transcript,
cnvs_json=json.dumps(cnvs_in_transcript),
cnvgenes = cnvs_per_gene,
cnvgenes_json=json.dumps(cnvs_per_gene)
)
cache.set(cache_key, t, timeout=1000*60)
print 'Rendering transcript: %s' % transcript_id
return t
except Exception, e:
print 'Failed on transcript:', transcript_id, ';Error=', traceback.format_exc()
abort(404)