def transcript_variants_subset_api(transcript_id):
try:
intervalset = IntervalSet.from_transcript(get_db(), transcript_id)
return _get_variants_subset_response_for_intervalset(intervalset)
except:
_err()
abort(500)
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 gene_variants_subset_api(gene_id):
try:
intervalset = IntervalSet.from_gene(get_db(), gene_id)
return _get_variants_subset_response_for_intervalset(intervalset)
except:
_err()
abort(500)
def variant_page(variant_id):
db = get_db()
try:
_log()
variant = lookups.get_variant_by_variant_id(
db, variant_id, default_to_boring_variant=False)
if not variant:
return not_found_page(
'The requested variant {!s} could not be found.'.format(
variant_id))
pop_names = {
k + '_AF': '1000G ' + v
for k, v in {
'AFR': 'African',
'AMR': 'American',
'EAS': 'East Asian',
'EUR': 'European',
'SAS': 'South Asian'
}.items()
}
if 'pop_afs' in variant:
variant['pop_afs'] = {
pop_names.get(k, k): v
for k, v in variant['pop_afs'].items()
}
else:
variant['pop_afs'] = {x: None for x in pop_names.itervalues()}
variant['pop_afs'][app.config['DATASET_NAME']] = variant['allele_freq']
consequence_drilldown = ConsequenceDrilldown.from_variant(variant)
gene_for_top_csq, top_HGVSs = ConsequenceDrilldown.get_top_gene_and_HGVSs(
consequence_drilldown)
consequence_drilldown_columns = ConsequenceDrilldown.split_into_two_columns(
consequence_drilldown)
base_coverage = get_coverage_handler().get_coverage_for_intervalset(
IntervalSet.from_xstart_xstop(
variant['xpos'], variant['xpos'] + len(variant['ref']) - 1))
metrics = lookups.get_metrics(db)
variant['quality_metrics']['QUAL'] = variant['site_quality']
lookups.remove_some_extraneous_information(variant)
return render_template(
'variant.html',
variant=variant,
base_coverage=base_coverage,
consequences=consequence_drilldown,
consequence_columns=consequence_drilldown_columns,
any_covered=bool(base_coverage),
metrics=metrics,
top_HGVSs=top_HGVSs,
gene_for_top_csq=gene_for_top_csq,
)
except:
_err()
abort(500)
def transcript_coverage_api(transcript_id):
try:
intervalset = IntervalSet.from_transcript(get_db(), transcript_id)
return jsonify(
get_coverage_handler().get_coverage_for_intervalset(intervalset))
except:
_err()
abort(500)
def gene_coverage_api(gene_id):
try:
intervalset = IntervalSet.from_gene(get_db(), gene_id)
return jsonify(
get_coverage_handler().get_coverage_for_intervalset(intervalset))
except:
_err()
abort(500)
def transcript_summary_api(transcript_id):
try:
intervalset = IntervalSet.from_transcript(get_db(), transcript_id)
return jsonify(
lookups.get_summary_for_intervalset(get_db(), intervalset))
except:
_err()
abort(500)
def gene_summary_api(gene_id):
try:
intervalset = IntervalSet.from_gene(get_db(), gene_id)
return jsonify(
lookups.get_summary_for_intervalset(get_db(), intervalset))
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 download_transcript_variants(transcript_id):
db = get_db()
try:
intervalset = IntervalSet.from_transcript(get_db(), transcript_id)
return _get_variants_csv_for_intervalset(
intervalset, '{}.csv'.format(transcript_id))
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)
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 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 download_gene_variants(gene_id):
db = get_db()
try:
intervalset = IntervalSet.from_gene(get_db(), gene_id)
return _get_variants_csv_for_intervalset(intervalset, '{}.csv'.format(gene_id))
except:_err(); abort(500)