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 variant_page(variant_str):
db = get_db()
try:
chrom, pos, ref, alt = variant_str.split('-')
pos = int(pos)
# pos, ref, alt = get_minimal_representation(pos, ref, alt)
xpos = xbrowse.get_xpos(chrom, pos)
variant = lookups.get_variant(db, xpos, ref, alt)
if variant is None:
variant = {
'chrom': chrom,
'pos': pos,
'xpos': xpos,
'ref': ref,
'alt': alt
}
consequences = None
ordered_csqs = None
if 'vep_annotations' in variant:
variant['vep_annotations'] = order_vep_by_csq(
variant['vep_annotations']) # Adds major_consequence
ordered_csqs = [
x['major_consequence'] for x in variant['vep_annotations']
]
ordered_csqs = reduce(
lambda x, y: ','.join([x, y]) if y not in x else x,
ordered_csqs, '').split(',') # Close but not quite there
consequences = defaultdict(lambda: defaultdict(list))
for annotation in variant['vep_annotations']:
annotation['HGVS'] = get_proper_hgvs(annotation)
consequences[annotation['major_consequence']][
annotation['Gene']].append(annotation)
base_coverage = lookups.get_coverage_for_bases(db, xpos,
xpos + len(ref) - 1)
any_covered = any([x['has_coverage'] for x in base_coverage])
metrics = lookups.get_metrics(db, variant)
print 'Rendering variant: %s' % variant_str
return render_template('variant.html',
variant=variant,
base_coverage=base_coverage,
consequences=consequences,
any_covered=any_covered,
ordered_csqs=ordered_csqs,
metrics=metrics)
except Exception, e:
print 'Failed on variant:', variant_str, '; Error=', traceback.format_exc(
)
abort(404)
def variant_data(variant_str, source):
db = get_db()
chrom, pos, ref, alt = variant_str.split('-')
pos = int(pos)
# pos, ref, alt = get_minimal_representation(pos, ref, alt)
xpos = get_xpos(chrom, pos)
variant = lookups.get_variant(db, source, xpos, ref, alt)
if variant is None:
variant = {
'chrom': chrom,
'pos': pos,
'xpos': xpos,
'ref': ref,
'alt': alt
}
consequences = OrderedDict()
if 'vep_annotations' in variant:
add_consequence_to_variant(variant)
variant['vep_annotations'] = remove_extraneous_vep_annotations(variant['vep_annotations'])
variant['vep_annotations'] = order_vep_by_csq(variant['vep_annotations']) # Adds major_consequence
for annotation in variant['vep_annotations']:
annotation['HGVS'] = get_proper_hgvs(annotation)
consequences.setdefault(annotation['major_consequence'], {}).setdefault(annotation['Gene'], []).append(annotation)
base_coverage = lookups.get_coverage_for_bases(db, 'base_coverage', xpos, xpos + len(ref) - 1)
any_covered = any([x['has_coverage'] for x in base_coverage])
metrics = lookups.get_metrics(db, variant)
# check the appropriate sqlite db to get the *expected* number of
# available bams and *actual* number of available bams for this variant
sqlite_db_path = os.path.join(
app.config["READ_VIZ_DIR"],
"combined_bams",
chrom,
"combined_chr%s_%03d.db" % (chrom, pos % 1000))
logging.info(sqlite_db_path)
try:
read_viz_db = sqlite3.connect(sqlite_db_path)
n_het = read_viz_db.execute("select n_expected_samples, n_available_samples from t "
"where chrom=? and pos=? and ref=? and alt=? and het_or_hom_or_hemi=?", (chrom, pos, ref, alt, 'het')).fetchone()
n_hom = read_viz_db.execute("select n_expected_samples, n_available_samples from t "
"where chrom=? and pos=? and ref=? and alt=? and het_or_hom_or_hemi=?", (chrom, pos, ref, alt, 'hom')).fetchone()
n_hemi = read_viz_db.execute("select n_expected_samples, n_available_samples from t "
"where chrom=? and pos=? and ref=? and alt=? and het_or_hom_or_hemi=?", (chrom, pos, ref, alt, 'hemi')).fetchone()
read_viz_db.close()
except Exception, e:
logging.error("Error when accessing sqlite db: %s - %s", sqlite_db_path, e)
n_het = n_hom = n_hemi = None
def variant_page(variant_str):
db = get_db()
try:
chrom, pos, ref, alt = variant_str.split('-')
pos = int(pos)
# pos, ref, alt = get_minimal_representation(pos, ref, alt)
xpos = xbrowse.get_xpos(chrom, pos)
variant = lookups.get_variant(db, xpos, ref, alt)
if variant is None:
variant = {
'chrom': chrom,
'pos': pos,
'xpos': xpos,
'ref': ref,
'alt': alt
}
consequences = None
ordered_csqs = None
if 'vep_annotations' in variant:
variant['vep_annotations'] = order_vep_by_csq(variant['vep_annotations']) # Adds major_consequence
ordered_csqs = [x['major_consequence'] for x in variant['vep_annotations']]
ordered_csqs = reduce(lambda x, y: ','.join([x, y]) if y not in x else x, ordered_csqs, '').split(',') # Close but not quite there
consequences = defaultdict(lambda: defaultdict(list))
for annotation in variant['vep_annotations']:
annotation['HGVS'] = get_proper_hgvs(annotation)
consequences[annotation['major_consequence']][annotation['Gene']].append(annotation)
base_coverage = lookups.get_coverage_for_bases(db, xpos, xpos + len(ref) - 1)
any_covered = any([x['has_coverage'] for x in base_coverage])
metrics = lookups.get_metrics(db, variant)
print 'Rendering variant: %s' % variant_str
return render_template(
'variant.html',
variant=variant,
base_coverage=base_coverage,
consequences=consequences,
any_covered=any_covered,
ordered_csqs=ordered_csqs,
metrics=metrics
)
except Exception, e:
print 'Failed on variant:', variant_str, '; Error=', traceback.format_exc()
abort(404)
def variant_page(variant_str):
db = get_db()
try:
chrom, pos, ref, alt = variant_str.split("-")
pos = int(pos)
# pos, ref, alt = get_minimal_representation(pos, ref, alt)
xpos = get_xpos(chrom, pos)
variant = lookups.get_variant(db, xpos, ref, alt)
if variant is None:
variant = {"chrom": chrom, "pos": pos, "xpos": xpos, "ref": ref, "alt": alt}
consequences = None
ordered_csqs = None
if "vep_annotations" in variant:
variant["vep_annotations"] = order_vep_by_csq(variant["vep_annotations"]) # Adds major_consequence
ordered_csqs = [x["major_consequence"] for x in variant["vep_annotations"]]
ordered_csqs = reduce(lambda x, y: ",".join([x, y]) if y not in x else x, ordered_csqs, "").split(
","
) # Close but not quite there
consequences = defaultdict(lambda: defaultdict(list))
for annotation in variant["vep_annotations"]:
annotation["HGVS"] = get_proper_hgvs(annotation)
consequences[annotation["major_consequence"]][annotation["Gene"]].append(annotation)
base_coverage = lookups.get_coverage_for_bases(db, xpos, xpos + len(ref) - 1)
any_covered = any([x["has_coverage"] for x in base_coverage])
metrics = lookups.get_metrics(db, variant)
print "Rendering variant: %s" % variant_str
return render_template(
"variant.html",
variant=variant,
base_coverage=base_coverage,
consequences=consequences,
any_covered=any_covered,
ordered_csqs=ordered_csqs,
metrics=metrics,
)
except Exception, e:
print "Failed on variant:", variant_str, "; Error=", traceback.format_exc()
abort(404)
def variant_page(variant_str):
db = get_db()
try:
chrom, pos, ref, alt = variant_str.split('-')
pos = int(pos)
# pos, ref, alt = get_minimal_representation(pos, ref, alt)
xpos = get_xpos(chrom, pos)
variant = lookups.get_variant(db, xpos, ref, alt)
if variant is None:
variant = {
'chrom': chrom,
'pos': pos,
'xpos': xpos,
'ref': ref,
'alt': alt
}
consequences = OrderedDict()
if 'vep_annotations' in variant:
add_consequence_to_variant(variant)
variant['vep_annotations'] = remove_extraneous_vep_annotations(variant['vep_annotations'])
variant['vep_annotations'] = order_vep_by_csq(variant['vep_annotations']) # Adds major_consequence
for annotation in variant['vep_annotations']:
annotation['HGVS'] = get_proper_hgvs(annotation)
consequences.setdefault(annotation['major_consequence'], {}).setdefault(annotation['Gene'], []).append(annotation)
base_coverage = lookups.get_coverage_for_bases(db, xpos, xpos + len(ref) - 1)
any_covered = any([x['has_coverage'] for x in base_coverage])
metrics = lookups.get_metrics(db, variant)
# check the appropriate sqlite db to get the *expected* number of
# available bams and *actual* number of available bams for this variant
sqlite_db_path = os.path.join(
app.config["READ_VIZ_DIR"],
"combined_bams",
chrom,
"combined_chr%s_%03d.db" % (chrom, pos % 1000))
logging.info(sqlite_db_path)
try:
read_viz_db = sqlite3.connect(sqlite_db_path)
n_het = read_viz_db.execute("select n_expected_samples, n_available_samples from t "
"where chrom=? and pos=? and ref=? and alt=? and het_or_hom_or_hemi=?", (chrom, pos, ref, alt, 'het')).fetchone()
n_hom = read_viz_db.execute("select n_expected_samples, n_available_samples from t "
"where chrom=? and pos=? and ref=? and alt=? and het_or_hom_or_hemi=?", (chrom, pos, ref, alt, 'hom')).fetchone()
n_hemi = read_viz_db.execute("select n_expected_samples, n_available_samples from t "
"where chrom=? and pos=? and ref=? and alt=? and het_or_hom_or_hemi=?", (chrom, pos, ref, alt, 'hemi')).fetchone()
read_viz_db.close()
except Exception, e:
logging.error("Error when accessing sqlite db: %s - %s", sqlite_db_path, e)
n_het = n_hom = n_hemi = None
read_viz_dict = {
'het': {'n_expected': n_het[0] if n_het is not None and n_het[0] is not None else 0,
'n_available': n_het[1] if n_het is not None and n_het[1] is not None else 0,},
'hom': {'n_expected': n_hom[0] if n_hom is not None and n_hom[0] is not None else 0,
'n_available': n_hom[1] if n_hom is not None and n_hom[1] is not None else 0,},
'hemi': {'n_expected': n_hemi[0] if n_hemi is not None and n_hemi[0] is not None else 0,
'n_available': n_hemi[1] if n_hemi is not None and n_hemi[1] is not None else 0,},
}
total_available = 0
total_expected = 0
for het_or_hom_or_hemi in ('het', 'hom', 'hemi'):
total_available += read_viz_dict[het_or_hom_or_hemi]['n_available']
total_expected += read_viz_dict[het_or_hom_or_hemi]['n_expected']
read_viz_dict[het_or_hom_or_hemi]['readgroups'] = [
'%(chrom)s-%(pos)s-%(ref)s-%(alt)s_%(het_or_hom_or_hemi)s%(i)s' % locals()
for i in range(read_viz_dict[het_or_hom_or_hemi]['n_available'])
] #eg. '1-157768000-G-C_hom1',
read_viz_dict[het_or_hom_or_hemi]['urls'] = [
#os.path.join('combined_bams', chrom, 'combined_chr%s_%03d.bam' % (chrom, pos % 1000))
os.path.join('combined_bams', chrom, 'combined_chr%s_%03d.bam' % (chrom, pos % 1000))
for i in range(read_viz_dict[het_or_hom_or_hemi]['n_available'])
]
read_viz_dict['total_available'] = total_available
read_viz_dict['total_expected'] = total_expected
print 'Rendering variant: %s' % variant_str
return render_template(
'variant.html',
variant=variant,
base_coverage=base_coverage,
consequences=consequences,
any_covered=any_covered,
metrics=metrics,
read_viz=read_viz_dict,
)
def variant_page(variant_str):
db = get_db()
try:
chrom, pos, ref, alt = variant_str.split('-')
pos = int(pos)
# pos, ref, alt = get_minimal_representation(pos, ref, alt)
xpos = get_xpos(chrom, pos)
variant = lookups.get_variant(db, xpos, ref, alt)
if variant is None:
variant = {
'chrom': chrom,
'pos': pos,
'xpos': xpos,
'ref': ref,
'alt': alt
}
consequences = OrderedDict()
if 'vep_annotations' in variant:
add_consequence_to_variant(variant)
variant['vep_annotations'] = remove_extraneous_vep_annotations(
variant['vep_annotations'])
variant['vep_annotations'] = order_vep_by_csq(
variant['vep_annotations']) # Adds major_consequence
for annotation in variant['vep_annotations']:
annotation['HGVS'] = get_proper_hgvs(annotation)
consequences.setdefault(annotation['major_consequence'],
{}).setdefault(annotation['Gene'],
[]).append(annotation)
base_coverage = lookups.get_coverage_for_bases(db, xpos,
xpos + len(ref) - 1)
any_covered = any([x['has_coverage'] for x in base_coverage])
metrics = lookups.get_metrics(db, variant)
# check the appropriate sqlite db to get the *expected* number of
# available bams and *actual* number of available bams for this variant
sqlite_db_path = os.path.join(
app.config["READ_VIZ_DIR"], "combined_bams", chrom,
"combined_chr%s_%03d.db" % (chrom, pos % 1000))
logging.info(sqlite_db_path)
try:
read_viz_db = sqlite3.connect(sqlite_db_path)
n_het = read_viz_db.execute(
"select n_expected_samples, n_available_samples from t "
"where chrom=? and pos=? and ref=? and alt=? and het_or_hom_or_hemi=?",
(chrom, pos, ref, alt, 'het')).fetchone()
n_hom = read_viz_db.execute(
"select n_expected_samples, n_available_samples from t "
"where chrom=? and pos=? and ref=? and alt=? and het_or_hom_or_hemi=?",
(chrom, pos, ref, alt, 'hom')).fetchone()
n_hemi = read_viz_db.execute(
"select n_expected_samples, n_available_samples from t "
"where chrom=? and pos=? and ref=? and alt=? and het_or_hom_or_hemi=?",
(chrom, pos, ref, alt, 'hemi')).fetchone()
read_viz_db.close()
except Exception, e:
logging.error("Error when accessing sqlite db: %s - %s",
sqlite_db_path, e)
n_het = n_hom = n_hemi = None
read_viz_dict = {
'het': {
'n_expected':
n_het[0] if n_het is not None and n_het[0] is not None else 0,
'n_available':
n_het[1] if n_het is not None and n_het[1] is not None else 0,
},
'hom': {
'n_expected':
n_hom[0] if n_hom is not None and n_hom[0] is not None else 0,
'n_available':
n_hom[1] if n_hom is not None and n_hom[1] is not None else 0,
},
'hemi': {
'n_expected':
n_hemi[0]
if n_hemi is not None and n_hemi[0] is not None else 0,
'n_available':
n_hemi[1]
if n_hemi is not None and n_hemi[1] is not None else 0,
},
}
total_available = 0
total_expected = 0
for het_or_hom_or_hemi in ('het', 'hom', 'hemi'):
total_available += read_viz_dict[het_or_hom_or_hemi]['n_available']
total_expected += read_viz_dict[het_or_hom_or_hemi]['n_expected']
read_viz_dict[het_or_hom_or_hemi]['readgroups'] = [
'%(chrom)s-%(pos)s-%(ref)s-%(alt)s_%(het_or_hom_or_hemi)s%(i)s'
% locals() for i in range(read_viz_dict[het_or_hom_or_hemi]
['n_available'])
] #eg. '1-157768000-G-C_hom1',
read_viz_dict[het_or_hom_or_hemi]['urls'] = [
#os.path.join('combined_bams', chrom, 'combined_chr%s_%03d.bam' % (chrom, pos % 1000))
os.path.join('combined_bams', chrom,
'combined_chr%s_%03d.bam' % (chrom, pos % 1000))
for i in range(read_viz_dict[het_or_hom_or_hemi]
['n_available'])
]
read_viz_dict['total_available'] = total_available
read_viz_dict['total_expected'] = total_expected
print 'Rendering variant: %s' % variant_str
return render_template(
'variant.html',
variant=variant,
base_coverage=base_coverage,
consequences=consequences,
any_covered=any_covered,
metrics=metrics,
read_viz=read_viz_dict,
)
def variant_page(variant_str):
db = get_db()
try:
chrom, pos, ref, alt = variant_str.split('-')
pos = int(pos)
# pos, ref, alt = get_minimal_representation(pos, ref, alt)
xpos = get_xpos(chrom, pos)
variant = lookups.get_variant(db, xpos, ref, alt)
if variant is None:
variant = {
'chrom': chrom,
'pos': pos,
'xpos': xpos,
'ref': ref,
'alt': alt
}
consequences = None
ordered_csqs = None
if 'vep_annotations' in variant:
variant['vep_annotations'] = order_vep_by_csq(
variant['vep_annotations']) # Adds major_consequence
ordered_csqs = [
x['major_consequence'] for x in variant['vep_annotations']
]
ordered_csqs = reduce(
lambda x, y: ','.join([x, y]) if y not in x else x,
ordered_csqs, '').split(',') # Close but not quite there
consequences = defaultdict(lambda: defaultdict(list))
for annotation in variant['vep_annotations']:
annotation['HGVS'] = get_proper_hgvs(annotation)
consequences[annotation['major_consequence']][
annotation['Gene']].append(annotation)
base_coverage = lookups.get_coverage_for_bases(db, xpos,
xpos + len(ref) - 1)
any_covered = any([x['has_coverage'] for x in base_coverage])
metrics = lookups.get_metrics(db, variant)
# check the appropriate sqlite db to get the *expected* number of
# available bams and *actual* number of available bams for this variant
sqlite_db_path = os.path.join(
app.config["READ_VIZ_DIR"], "combined_bams", chrom,
"combined_chr%s_%03d.db" % (chrom, pos % 1000))
print(sqlite_db_path)
try:
read_viz_db = sqlite3.connect(sqlite_db_path)
n_het = read_viz_db.execute(
"select n_expected_samples, n_available_samples from t "
"where chrom=? and pos=? and ref=? and alt=? and het_or_hom=?",
(chrom, pos, ref, alt, 'het')).fetchone()
n_hom = read_viz_db.execute(
"select n_expected_samples, n_available_samples from t "
"where chrom=? and pos=? and ref=? and alt=? and het_or_hom=?",
(chrom, pos, ref, alt, 'hom')).fetchone()
read_viz_db.close()
except Exception, e:
logging.debug("Error when accessing sqlite db: %s - %s",
sqlite_db_path, e)
n_het = n_hom = None
read_viz_dict = {
'het': {
'n_expected':
n_het[0] if n_het is not None and n_het[0] is not None else -1,
'n_available':
n_het[1] if n_het and n_het[1] else 0,
},
'hom': {
'n_expected':
n_hom[0] if n_hom is not None and n_hom[0] is not None else -1,
'n_available':
n_hom[1] if n_hom and n_hom[1] else 0,
},
}
for het_or_hom in (
'het',
'hom',
):
#read_viz_dict[het_or_hom]['some_samples_missing'] = (read_viz_dict[het_or_hom]['n_expected'] > 0) and (read_viz_dict[het_or_hom]['n_expected'] - read_viz_dict[het_or_hom]['n_available'] > 0)
read_viz_dict[het_or_hom]['all_samples_missing'] = (
read_viz_dict[het_or_hom]['n_expected'] !=
0) and (read_viz_dict[het_or_hom]['n_available'] == 0)
read_viz_dict[het_or_hom]['readgroups'] = [
'%(chrom)s-%(pos)s-%(ref)s-%(alt)s_%(het_or_hom)s%(i)s' %
locals()
for i in range(read_viz_dict[het_or_hom]['n_available'])
] #eg. '1-157768000-G-C_hom1',
read_viz_dict[het_or_hom]['urls'] = [
os.path.join('combined_bams', chrom,
'combined_chr%s_%03d.bam' % (chrom, pos % 1000))
for i in range(read_viz_dict[het_or_hom]['n_available'])
]
print 'Rendering variant: %s' % variant_str
return render_template(
'variant.html',
variant=variant,
base_coverage=base_coverage,
consequences=consequences,
any_covered=any_covered,
ordered_csqs=ordered_csqs,
metrics=metrics,
read_viz=read_viz_dict,
)
def variant_page(variant_str):
db = get_db()
try:
chrom, pos, ref, alt = variant_str.split("-")
pos = int(pos)
# pos, ref, alt = get_minimal_representation(pos, ref, alt)
xpos = get_xpos(chrom, pos)
variant = lookups.get_variant(db, xpos, ref, alt)
if variant is None:
variant = {"chrom": chrom, "pos": pos, "xpos": xpos, "ref": ref, "alt": alt}
consequences = None
ordered_csqs = None
if "vep_annotations" in variant:
variant["vep_annotations"] = order_vep_by_csq(variant["vep_annotations"]) # Adds major_consequence
ordered_csqs = [x["major_consequence"] for x in variant["vep_annotations"]]
ordered_csqs = reduce(lambda x, y: ",".join([x, y]) if y not in x else x, ordered_csqs, "").split(
","
) # Close but not quite there
consequences = defaultdict(lambda: defaultdict(list))
for annotation in variant["vep_annotations"]:
annotation["HGVS"] = get_proper_hgvs(annotation)
consequences[annotation["major_consequence"]][annotation["Gene"]].append(annotation)
base_coverage = lookups.get_coverage_for_bases(db, xpos, xpos + len(ref) - 1)
any_covered = any([x["has_coverage"] for x in base_coverage])
metrics = lookups.get_metrics(db, variant)
# check the appropriate sqlite db to get the *expected* number of
# available bams and *actual* number of available bams for this variant
sqlite_db_path = os.path.join(
app.config["READ_VIZ_DIR"], "combined_bams", chrom, "combined_chr%s_%03d.db" % (chrom, pos % 1000)
)
print (sqlite_db_path)
try:
read_viz_db = sqlite3.connect(sqlite_db_path)
n_het = read_viz_db.execute(
"select n_expected_samples, n_available_samples from t "
"where chrom=? and pos=? and ref=? and alt=? and het_or_hom=?",
(chrom, pos, ref, alt, "het"),
).fetchone()
n_hom = read_viz_db.execute(
"select n_expected_samples, n_available_samples from t "
"where chrom=? and pos=? and ref=? and alt=? and het_or_hom=?",
(chrom, pos, ref, alt, "hom"),
).fetchone()
read_viz_db.close()
except Exception, e:
logging.debug("Error when accessing sqlite db: %s - %s", sqlite_db_path, e)
n_het = n_hom = None
read_viz_dict = {
"het": {
"n_expected": n_het[0] if n_het is not None and n_het[0] is not None else -1,
"n_available": n_het[1] if n_het and n_het[1] else 0,
},
"hom": {
"n_expected": n_hom[0] if n_hom is not None and n_hom[0] is not None else -1,
"n_available": n_hom[1] if n_hom and n_hom[1] else 0,
},
}
for het_or_hom in ("het", "hom"):
# read_viz_dict[het_or_hom]['some_samples_missing'] = (read_viz_dict[het_or_hom]['n_expected'] > 0) and (read_viz_dict[het_or_hom]['n_expected'] - read_viz_dict[het_or_hom]['n_available'] > 0)
read_viz_dict[het_or_hom]["all_samples_missing"] = (read_viz_dict[het_or_hom]["n_expected"] != 0) and (
read_viz_dict[het_or_hom]["n_available"] == 0
)
read_viz_dict[het_or_hom]["readgroups"] = [
"%(chrom)s-%(pos)s-%(ref)s-%(alt)s_%(het_or_hom)s%(i)s" % locals()
for i in range(read_viz_dict[het_or_hom]["n_available"])
] # eg. '1-157768000-G-C_hom1',
read_viz_dict[het_or_hom]["urls"] = [
os.path.join("combined_bams", chrom, "combined_chr%s_%03d.bam" % (chrom, pos % 1000))
for i in range(read_viz_dict[het_or_hom]["n_available"])
]
print "Rendering variant: %s" % variant_str
return render_template(
"variant.html",
variant=variant,
base_coverage=base_coverage,
consequences=consequences,
any_covered=any_covered,
ordered_csqs=ordered_csqs,
metrics=metrics,
read_viz=read_viz_dict,
)
def variant_page(variant_str):
db = get_db()
try:
chrom, pos, ref, alt = variant_str.split('-')
pos = int(pos)
# pos, ref, alt = get_minimal_representation(pos, ref, alt)
xpos = get_xpos(chrom, pos)
variant = lookups.get_variant(db, xpos, ref, alt)
if variant is None:
variant = {
'chrom': chrom,
'pos': pos,
'xpos': xpos,
'ref': ref,
'alt': alt
}
consequences = None
ordered_csqs = None
if 'vep_annotations' in variant:
variant['vep_annotations'] = order_vep_by_csq(variant['vep_annotations']) # Adds major_consequence
ordered_csqs = [x['major_consequence'] for x in variant['vep_annotations']]
ordered_csqs = reduce(lambda x, y: ','.join([x, y]) if y not in x else x, ordered_csqs, '').split(',') # Close but not quite there
consequences = defaultdict(lambda: defaultdict(list))
for annotation in variant['vep_annotations']:
annotation['HGVS'] = get_proper_hgvs(annotation)
consequences[annotation['major_consequence']][annotation['Gene']].append(annotation)
base_coverage = lookups.get_coverage_for_bases(db, xpos, xpos + len(ref) - 1)
any_covered = any([x['has_coverage'] for x in base_coverage])
metrics = lookups.get_metrics(db, variant)
# check the appropriate sqlite db to get the *expected* number of
# available bams and *actual* number of available bams for this variant
sqlite_db_path = os.path.join(
app.config["READ_VIZ_DIR"],
"combined_bams",
chrom,
"combined_chr%s_%03d.db" % (chrom, pos % 1000))
print(sqlite_db_path)
try:
read_viz_db = sqlite3.connect(sqlite_db_path)
n_het = read_viz_db.execute("select n_expected_samples, n_available_samples from t "
"where chrom=? and pos=? and ref=? and alt=? and het_or_hom=?", (chrom, pos, ref, alt, 'het')).fetchone()
n_hom = read_viz_db.execute("select n_expected_samples, n_available_samples from t "
"where chrom=? and pos=? and ref=? and alt=? and het_or_hom=?", (chrom, pos, ref, alt, 'hom')).fetchone()
read_viz_db.close()
except Exception, e:
logging.debug("Error when accessing sqlite db: %s - %s", sqlite_db_path, e)
n_het = n_hom = None
read_viz_dict = {
'het': {'n_expected': n_het[0] if n_het is not None and n_het[0] is not None else -1, 'n_available': n_het[1] if n_het and n_het[1] else 0,},
'hom': {'n_expected': n_hom[0] if n_hom is not None and n_hom[0] is not None else -1, 'n_available': n_hom[1] if n_hom and n_hom[1] else 0,},
}
for het_or_hom in ('het', 'hom',):
#read_viz_dict[het_or_hom]['some_samples_missing'] = (read_viz_dict[het_or_hom]['n_expected'] > 0) and (read_viz_dict[het_or_hom]['n_expected'] - read_viz_dict[het_or_hom]['n_available'] > 0)
read_viz_dict[het_or_hom]['all_samples_missing'] = (read_viz_dict[het_or_hom]['n_expected'] != 0) and (read_viz_dict[het_or_hom]['n_available'] == 0)
read_viz_dict[het_or_hom]['readgroups'] = [
'%(chrom)s-%(pos)s-%(ref)s-%(alt)s_%(het_or_hom)s%(i)s' % locals()
for i in range(read_viz_dict[het_or_hom]['n_available'])
] #eg. '1-157768000-G-C_hom1',
read_viz_dict[het_or_hom]['urls'] = [
os.path.join('combined_bams', chrom, 'combined_chr%s_%03d.bam' % (chrom, pos % 1000))
for i in range(read_viz_dict[het_or_hom]['n_available'])
]
print 'Rendering variant: %s' % variant_str
return render_template(
'variant.html',
variant=variant,
base_coverage=base_coverage,
consequences=consequences,
any_covered=any_covered,
ordered_csqs=ordered_csqs,
metrics=metrics,
read_viz=read_viz_dict,
)