def load(context, sample, group, name, group_name, threshold, bed_stream):
"""Load Sambamba output into the database for a sample."""
chanjo_db = ChanjoDB(uri=context.obj['database'])
source = os.path.abspath(bed_stream.name)
result = load_transcripts(bed_stream,
sample_id=sample,
group_id=group,
source=source,
threshold=threshold)
result.sample.name = name
result.sample.group_name = group_name
try:
chanjo_db.add(result.sample)
with click.progressbar(result.models,
length=result.count,
label='loading transcripts') as bar:
for tx_model in bar:
chanjo_db.add(tx_model)
chanjo_db.save()
except IntegrityError as error:
LOG.error('sample already loaded, rolling back')
LOG.debug(error.args[0])
chanjo_db.session.rollback()
context.abort()
def link(context, bed_stream):
"""Link related genomic elements."""
chanjo_db = ChanjoDB(uri=context.obj['database'])
result = link_elements(bed_stream)
with click.progressbar(result.models, length=result.count,
label='adding transcripts') as bar:
for tx_model in bar:
chanjo_db.add(tx_model)
try:
chanjo_db.save()
except IntegrityError:
LOG.exception('elements already linked?')
chanjo_db.session.rollback()
click.echo("use 'chanjo db setup --reset' to re-build")
context.abort()
def link(context, bed_stream):
"""Link related genomic elements."""
chanjo_db = ChanjoDB(uri=context.obj['database'])
result = link_elements(bed_stream)
with click.progressbar(result.models, length=result.count,
label='adding transcripts') as bar:
for tx_model in bar:
chanjo_db.add(tx_model)
try:
chanjo_db.save()
except IntegrityError:
log.exception('elements already linked?')
chanjo_db.session.rollback()
click.echo("use 'chanjo db setup --reset' to re-build")
context.abort()
def load(context, sample, group, name, group_name, threshold, bed_stream):
"""Load Sambamba output into the database for a sample."""
chanjo_db = ChanjoDB(uri=context.obj['database'])
source = os.path.abspath(bed_stream.name)
result = load_transcripts(bed_stream, sample_id=sample, group_id=group,
source=source, threshold=threshold)
result.sample.name = name
result.sample.group_name = group_name
try:
chanjo_db.add(result.sample)
with click.progressbar(result.models, length=result.count,
label='loading transcripts') as bar:
for tx_model in bar:
chanjo_db.add(tx_model)
chanjo_db.save()
except IntegrityError as error:
LOG.error('sample already loaded, rolling back')
LOG.debug(error.args[0])
chanjo_db.session.rollback()
context.abort()