def test_split_fastq():
parts = split_fastq(FASTQ_PATH)
assert parts['sample'] == 'ADM992A10'
assert parts['index'] == 'GAGCTGAA'
assert parts['lane'] == 2
assert parts['read'] == 1
assert parts['segment'] == 1
def add_symlink(self, fastq_file, symlink, reason='analysis'):
parts = split_fastq(fastq_file)
# fetch relevant unaligned record
run_dir = get_run_dir(fastq_file)
flowcell_id = extract_flowcell(run_dir)
unaligned_obj = self._get_unaligned(parts['sample'], flowcell_id)
fastq_obj = (self.db.query(FastqFile)
.filter_by(lane=parts['lane'], read=parts['read'],
segment=parts['segment'],
unaligned=unaligned_obj)
.one())
logger.debug('saving symlink to database')
symlink_obj = Symlink(path=symlink, reason=reason, original=fastq_obj)
self.add_commit(symlink_obj)
def post(self):
fastq_file = request.form['fastq_file']
symlink = request.form['symlink']
flowcell_id = request.form['flowcell_id']
reason = request.form.get('reason', 'analysis')
parts = split_fastq(fastq_file)
# fetch relevant spof record
spof_obj = utils.get_spof(flowcell_id, parts['sample'])
filters = dict(lane=parts['lane'], read=parts['read'],
segment=parts['segment'], spof=spof_obj)
fastq_obj = FastqFile.query.filter_by(**filters).one()
logger.debug('saving symlink to database')
symlink_obj = Symlink(path=symlink, reason=reason, original=fastq_obj)
utils.commit(symlink_obj)
return symlink_obj.to_json()
def add_fastq_file(fastq_file, sample_obj, spof_obj):
"""Add FASTQ-file to the database."""
parts = split_fastq(fastq_file)
common_params = dict(lane=parts['lane'], barcode=parts['index'],
segment=parts['segment'], spof=spof_obj,
sample=sample_obj)
fastq_obj, was_created = get_or_create(FastqFile, file_name=fastq_file,
read=parts['read'], **common_params)
# logger.debug('adding read partner')
# other_read = 2 if parts['read'] == 1 else 1
# fastq_partner = FastqFile.query.filter_by(read=other_read,
# **common_params).first()
# if fastq_partner:
# fastq_obj.sibling = fastq_partner
# fastq_partner.sibling = fastq_obj
return fastq_obj
def add_fastq_file(self, fastq_file, sample_obj, unaligned_obj):
parts = split_fastq(fastq_file)
common_params = dict(lane=parts['lane'], barcode=parts['index'],
segment=parts['segment'], unaligned=unaligned_obj,
sample=sample_obj)
(fastq_obj,
was_created) = self.db.get_or_create(FastqFile,
file_name=fastq_file,
read=parts['read'],
**common_params)
logger.debug('looking up FASTQ read partner')
other_read = 2 if parts['read'] == 1 else 1
fastq_partner = (self.db.query(FastqFile)
.filter_by(read=other_read, **common_params)
.first())
fastq_obj.sibling = fastq_partner
self.db.save()
if fastq_partner:
fastq_partner.sibling = fastq_obj
self.db.save()
return fastq_obj
def build_mip_fastq_path(fastq_base, fastq_path, flowcell_id, date):
parts = split_fastq(fastq_path)
mip_fastq = build_mip_fastq(date=date, flowcell=flowcell_id, **parts)
mip_fastq_path = path(fastq_base).normpath().joinpath(mip_fastq)
return mip_fastq_path