def get_patient_samples(id):
""" Get all gene samples for an individual """
list = VcfSampleCollection().get_by_individualid(id)
# add query string to fetch (status and filter by ids)
return jsonify(list)
def beacon_query(chrom, position, allele, reference):
""" Canonical Query1 """
# Validate parameters
result = VcfSampleCollection().get_variants_count(chrom, position, allele, reference)
return jsonify({"count":result})
def get_samples_list():
""" Retrieve a list of patient samples """
# TODO: Validate parameters, error handling, and logging
# TODO: Need to make this bounded (paging)
list = VcfSampleCollection().get_all()
return jsonify(list)
def import_vcf(file_id):
VcfFileCollection().update_by_id(file_id, {'status': 'processing'})
sample_count = 0
try:
stream = open(os.path.join(Settings.file_store, file_id + '.vcf'), 'r')
vcf_reader = vcf.Reader(stream)
samples = next(vcf_reader).samples
sample_count = len(samples)
stream.seek(0)
vcf_reader = vcf.Reader(stream)
for i in range(0, sample_count):
stream.seek(0)
vcf_reader = vcf.Reader(stream)
variants = list()
for record in vcf_reader:
sample = record.samples[i]
#TODO - there are better ways to handle this
# Do we need to store the reference for this query
allleles = []
if sample.gt_bases is not None:
alleles = re.split(r'[\\/|]', sample.gt_bases)
# remove duplicates
alleles = set(alleles)
for allele in alleles:
chrom = record.CHROM
# remove preceeding chr if exists
if (re.match('chr', chrom, re.I)):
chrom = chrom[3:].upper()
if chrom in ['1', '2', '3', '4', '5', '6', '7', '8', '9','10','11','12','13','14','15','16','17','18','19','20','21','22', 'X', 'Y', 'M' ]:
variants.append(chrom + '_' + str(record.POS) + '_' + allele)
VcfSampleCollection().add(
{
'fileid': file_id,
'variants': variants
})
except:
log.exception('error importing patient vcf')
VcfFileCollection().update_by_id(file_id,
{
'status': 'complete',
'samples': sample_count
})
log.info('import complete')
def upload_patient_samples(id):
"""
VCF file upload operation
"""
try:
# check if the post request has the file part
if 'file' not in request.files:
return jsonify({'error': 'no file in file part'})
log.info('request files - %s', request.files)
file = request.files['file']
# if user does not select file, browser also
# submit a empty part without filename
if file.filename == '':
log.error('patient upload file name is empty')
flash('No selected file')
return jsonify({'error': 'no file'})
# 1) VALIDATE FILE AND WRITE HEADER RECORD
# 2) SAVE FILE TO VCF STORAGE PATH
# 3) QUEUE IMPORT PROCESSING
# this is used to ensure we can safely use the filename sent to us
#filename = secure_filename(file.filename)
# load data from the stream into memory for processing
data = file.read()
stream = io.StringIO(data.decode('utf-8'))
vcf_reader = vcf.Reader(stream)
# This approach creates a document for each sample
samples = next(vcf_reader).samples
sample_count = len(samples)
stream.seek(0)
vcf_reader = vcf.Reader(stream)
for i in range(0, sample_count):
stream.seek(0)
vcf_reader = vcf.Reader(stream)
variants = list()
for record in vcf_reader:
sample = record.samples[i]
#TODO - there are better ways to handle this
# Do we need to store the reference for this query
# sample = record.samples[0]
alleles = []
if sample.gt_bases is not None:
log.info(sample.gt_bases)
alleles = re.split(r'[\\/|]', sample.gt_bases)
# remove duplicates
alleles = set(alleles)
for allele in alleles:
chrom = record.CHROM
# remove preceeding chr if exists
if (re.match('chr', chrom, re.I)):
chrom = chrom[3:]
if chrom in [
'1', '2', '3', '4', '5', '6', '7', '8', '9', '10',
'11', '12', '13', '14', '15', '16', '17', '18',
'19', '20', '21', '22', 'X', 'Y', 'M'
]:
variants.append(chrom + '_' + str(record.POS) + '_' +
allele)
# insert samples into the database
VcfSampleCollection().add({'patientId': id, 'variants': variants})
except:
log.exception('error importing patient vcf')
# TODO: change this to return import stats
return jsonify({'result': 'ok'})
def delete_sample(id):
""" Delete a VCF sample """
VcfSampleCollection().delete(id)
return jsonify({'result': 'ok'})