def popexist_db(existing_db, exon_lines):
result = link_elements(exon_lines)
existing_db.add(*result.models)
result = load_transcripts(exon_lines, sample_id="sample", group_id="group")
existing_db.add(result.sample)
existing_db.add(*result.models)
existing_db.save()
yield existing_db
def popexist_db(existing_db, exon_lines):
result = link_elements(exon_lines)
existing_db.add(*result.models)
result = load_transcripts(exon_lines, sample_id='sample', group_id='group')
existing_db.add(result.sample)
existing_db.add(*result.models)
existing_db.save()
yield existing_db
def populated_db(chanjo_db, exon_lines):
exon_lines = list(exon_lines)
result = link_elements(exon_lines)
chanjo_db.add(*result.models)
results = [
load_transcripts(exon_lines, sample_id="sample", group_id="group"),
load_transcripts(exon_lines, sample_id="sample2", group_id="group"),
]
for result in results:
chanjo_db.add(result.sample)
chanjo_db.add(*result.models)
chanjo_db.save()
yield chanjo_db
def populated_db(chanjo_db, exon_lines):
exon_lines = list(exon_lines)
result = link_elements(exon_lines)
chanjo_db.add(*result.models)
results = [
load_transcripts(exon_lines, sample_id='sample', group_id='group'),
load_transcripts(exon_lines, sample_id='sample2', group_id='group')
]
for result in results:
chanjo_db.add(result.sample)
chanjo_db.add(*result.models)
chanjo_db.save()
yield chanjo_db
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 test_process(bed_lines):
result = link.link_elements(bed_lines)
models = list(result.models)
assert result.count == 5 # 5 transcripts