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)
print 'Rendering %stranscript: %s' % ('' if t is None else 'cached ', transcript_id)
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)
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),
csq_order=csq_order,
)
cache.set(cache_key, t)
return t
except Exception, e:
print 'Failed on transcript:', transcript_id, ';Error=', traceback.format_exc()
abort(404)
def get_transcript_data(db, transcript_id, transcript, request_type, cache_key):
try:
gene = lookups.get_gene(db, transcript['gene_id'])
gene['transcripts'] = lookups.get_transcripts_in_gene(db, transcript['gene_id'])
variant_data = lookups.get_variants_in_gene_or_transcript(db, transcript_id=transcript_id)
variants_in_transcript = variant_data['all_variants']
coverage_stats_exomes = lookups.get_coverage_for_transcript(db, 'exome_coverage', transcript['xstart'] - EXON_PADDING, transcript['xstop'] + EXON_PADDING)
# change base_coverage to e.g. genome_base_coverage when the data gets here
coverage_stats_genomes = lookups.get_coverage_for_transcript(db, 'genome_coverage', transcript['xstart'] - EXON_PADDING, transcript['xstop'] + EXON_PADDING)
coverage_stats = {
'exomes': coverage_stats_exomes,
'genomes': coverage_stats_genomes
}
add_transcript_coordinate_to_variants(db, variants_in_transcript, transcript_id)
if request_type == 'template':
result = render_template(
'transcript.html',
transcript=transcript,
variants_in_transcript=variants_in_transcript,
coverage_stats=coverage_stats,
gene=gene,
)
if request_type == 'json':
result = jsonify(
transcript=transcript,
variants_in_transcript=variants_in_transcript,
coverage_stats=coverage_stats,
gene=gene,
)
cache.set(cache_key, result, timeout=1000*60)
return result
except Exception, e:
print 'Failed on transcript:', transcript_id, ';Error=', traceback.format_exc()
abort(404)
def text_page():
db = get_db()
query = request.args.get("text")
datatype, identifier = lookups.get_awesomebar_result(db, query)
if datatype in ["gene", "transcript"]:
gene = lookups.get_gene(db, identifier)
link = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr%(chrom)s%%3A%(start)s-%(stop)s" % gene
output = """Searched for %s. Found %s.
%s; Canonical: %s.
%s""" % (
query,
identifier,
gene["full_gene_name"],
gene["canonical_transcript"],
link,
)
output += (
""
if "omim_accession" not in gene
else """
In OMIM: %(omim_description)s
http://omim.org/entry/%(omim_accession)s"""
% gene
)
return output
elif datatype == "error" or datatype == "not_found":
return "Gene/transcript %s not found" % query
else:
return "Search types other than gene transcript not yet supported"
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)
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(
'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
)
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=', e
abort(404)
def gene_api(gene_id):
db = get_db()
gene = lookups.get_gene(db, gene_id)
if gene is None:
abort(404)
cache_key = 'json-gene-{}'.format(gene_id)
json = cache.get(cache_key)
if json is None:
json = get_gene_data(db, gene_id, gene, 'json', cache_key)
print 'Sending json for gene: %s' % gene_id
return json
def gene_page(gene_id):
db = get_db()
try:
gene = lookups.get_gene(db, gene_id)
if not gene: return not_found_page('The requested gene {!s} could not be found.'.format(gene_id))
_log(' ({})'.format(gene.get('gene_name')))
intervalset = IntervalSet.from_gene(db, gene_id)
genes = TranscriptSet.from_gene(db, gene_id).genes
return render_template(
'gene.html',
intervalset=intervalset, genes=genes, csq=Consequence.as_obj,
gene=gene,
)
except:_err(); abort(500)
def gene_page(gene_id):
if gene_id in GENES_TO_CACHE:
return open(os.path.join(GENE_CACHE_DIR, '{}.html'.format(gene_id))).read()
print 'accessing from gene page'
else:
db = get_db()
gene = lookups.get_gene(db, gene_id)
if gene is None:
abort(404)
cache_key = 'template-gene-{}'.format(gene_id)
template = cache.get(cache_key)
if template is None:
template = get_gene_data(db, gene_id, gene, 'template', cache_key)
print 'Rendering gene: %s' % gene_id
return template
def transcript_page(transcript_id):
db = get_db()
try:
_log()
transcript = lookups.get_transcript(db, transcript_id)
if not transcript: return not_found_page('The requested transcript {!s} could not be found.'.format(transcript_id))
gene = lookups.get_gene(db, transcript['gene_id'])
intervalset = IntervalSet.from_transcript(db, transcript_id)
genes = TranscriptSet.from_transcript(db, transcript_id).genes
return render_template(
'transcript.html',
intervalset=intervalset, genes=genes, csq=Consequence.as_obj,
gene=gene,
transcript=transcript,
)
except:_err(); abort(500)
def get_gene_page_content(gene_id):
dbname = session['db_selected']
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)
print 'Rendering %sgene: %s' % ('' if t is None else 'cached ',
gene_id)
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)
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,
constraint=constraint_info,
csq_order=csq_order,
dbname=dbname,
)
cache.set(cache_key, t)
return t
except Exception, e:
print 'Failed on gene:', gene_id, ';Error=', traceback.format_exc()
abort(404)
def text_page():
db = get_db()
query = request.args.get('text')
datatype, identifier = lookups.get_awesomebar_result(db, query)
if datatype in ['gene', 'transcript']:
gene = lookups.get_gene(db, identifier)
link = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr%(chrom)s%%3A%(start)s-%(stop)s" % gene
output = '''Searched for %s. Found %s.
%s; Canonical: %s.
%s''' % (query, identifier, gene['full_gene_name'], gene['canonical_transcript'], link)
output += '' if 'omim_accession' not in gene else '''
In OMIM: %(omim_description)s
http://omim.org/entry/%(omim_accession)s''' % gene
return output
elif datatype == 'error' or datatype == 'not_found':
return "Gene/transcript %s not found" % query
else:
return "Search types other than gene transcript not yet supported"
def text_page():
db = get_db()
query = request.args.get('text')
datatype, identifier = lookups.get_awesomebar_result(db, query)
if datatype in ['gene', 'transcript']:
gene = lookups.get_gene(db, identifier)
link = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr%(chrom)s%%3A%(start)s-%(stop)s" % gene
output = '''Searched for %s. Found %s.
%s; Canonical: %s.
%s''' % (query, identifier, gene['full_gene_name'], gene['canonical_transcript'], link)
output += '' if 'omim_accession' not in gene else '''
In OMIM: %(omim_description)s
http://omim.org/entry/%(omim_accession)s''' % gene
return output
elif datatype == 'error' or datatype == 'not_found':
return "Gene/transcript %s not found" % query
else:
return "Search types other than gene transcript not yet supported"
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 transcript_page(transcript_id):
dbname = session['db_selected']
db = get_db()
try:
transcript = lookups.get_transcript(db, transcript_id)
cache_key = 't-transcript-{}'.format(transcript_id)
t = cache.get(cache_key)
print 'Rendering %stranscript: %s' % ('' if t is None else 'cached ',
transcript_id)
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)
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),
csq_order=csq_order,
dbname=dbname,
)
cache.set(cache_key, t)
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)
print "Rendering %sgene: %s" % ("" if t is None else "cached ", gene_id)
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)
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,
constraint=constraint_info,
csq_order=csq_order,
)
cache.set(cache_key, t)
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)
print "Rendering %stranscript: %s" % ("" if t is None else "cached ", transcript_id)
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)
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),
csq_order=csq_order,
)
cache.set(cache_key, t)
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:
print "gene_id", gene_id
gene = lookups.get_gene(db, gene_id)
print "gene", gene
if gene is None:
abort(404)
gene_name = gene['gene_name']
print gene_name
variants_in_gene = lookups.get_variants_in_gene(db, gene_name)
transcripts_in_gene = lookups.get_transcripts_in_gene(db, gene_id)
transcript_id = gene['canonical_transcript']
transcript = lookups.get_transcript(db, transcript_id)
variants_in_transcript = lookups.get_variants_in_transcript(
db, transcript_id)
add_transcript_coordinate_to_variants(db, variants_in_transcript,
transcript_id)
#print gene
#print variants_in_gene
#print transcript
#print transcripts_in_gene
#print "variants_in_transcript\n",variants_in_transcript
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)
print 'Rendering gene: %s' % gene_id
return t
except Exception, e:
print 'Failed on gene:', gene_id, ';Error=', traceback.format_exc()
abort(404)