def test_exporter_pipeline():
# set up
chanjo_db = Store(':memory:')
chanjo_db.set_up()
chanjo_db.add(
chanjo_db.create('interval',
interval_id='intervalY',
contig='Y',
start=123,
end=501,
strand='-'))
chanjo_db.save()
bed_lines = list(export_intervals(chanjo_db))
assert bed_lines[0] == '#chrom\tchromStart\tchromEnd\tname\tscore\tstrand'
assert bed_lines[1:] == ['Y\t122\t501\tintervalY\t0\t-']
def test_fetch_records():
# set up
chanjo_db = Store(':memory:')
chanjo_db.set_up()
chanjo_db.add(
chanjo_db.create('interval',
interval_id='interval1',
contig='chr1',
start=10,
end=100,
strand='+'))
chanjo_db.save()
columns = (Interval.contig, Interval.start, Interval.end)
intervals = list(fetch_records(chanjo_db, columns))
assert len(intervals) == 1
assert intervals[0] == ('chr1', 10, 100)
def test_exporter_pipeline():
# set up
chanjo_db = Store(':memory:')
chanjo_db.set_up()
chanjo_db.add(chanjo_db.create(
'interval',
interval_id='intervalY',
contig='Y',
start=123,
end=501,
strand='-'
))
chanjo_db.save()
bed_lines = list(export_intervals(chanjo_db))
assert bed_lines[0] == '#chrom\tchromStart\tchromEnd\tname\tscore\tstrand'
assert bed_lines[1:] == ['Y\t122\t501\tintervalY\t0\t-']
def test_fetch_records():
# set up
chanjo_db = Store(':memory:')
chanjo_db.set_up()
chanjo_db.add(chanjo_db.create(
'interval',
interval_id='interval1',
contig='chr1',
start=10,
end=100,
strand='+'
))
chanjo_db.save()
columns = (Interval.contig, Interval.start, Interval.end)
intervals = list(fetch_records(chanjo_db, columns))
assert len(intervals) == 1
assert intervals[0] == ('chr1', 10, 100)
def link(context, transcripts, bed_stream):
"""Link related genomic elements."""
only_tx = transcripts or context.obj.get('transcripts') or False
base = TXBASE if only_tx else BASE
chanjo_db = Store(uri=context.obj['database'], base=base)
try:
if only_tx:
result = load.link_transcripts(bed_stream)
with click.progressbar(result.models,
length=result.count,
label='adding transcripts') as bar:
for tx_model in bar:
chanjo_db.session.add(tx_model)
chanjo_db.save()
else:
link_elements(chanjo_db, bed_stream)
except IntegrityError:
click.echo("elements already linked, use 'chanjo db setup --reset' "
"to re-build")
class TestBuildElement(object):
def setup(self):
self.store = Store(':memory:')
self.store.set_up()
self.interval = BaseInterval('1',
10,
100,
name='int1',
block_ids=['block1', 'block2'],
superblock_ids=['sblock1', 'sblock1'])
self.db_interval = StoreInterval(interval_id=self.interval.name,
contig=self.interval.contig,
start=self.interval.start,
end=self.interval.end,
strand=self.interval.strand)
self.interval_group = [('block2', self.db_interval, 'sblock1')]
def test_build_interval(self):
intervals = list(build_interval(self.store, self.interval))
self.store.save()
new_interval = self.store.get('interval', self.interval.name)
assert new_interval.id == self.interval.name
assert new_interval.start == self.interval.start
assert len(intervals) == 2
def test_build_block(self):
superblock_id, new_block = build_block(self.store, self.interval_group)
self.store.save()
db_block = self.store.get('block', self.interval_group[0][0])
assert superblock_id == 'sblock1'
assert new_block.id == db_block.id == self.interval_group[0][0]
assert new_block.start == db_block.start == self.interval_group[0][
1].start
class TestBuildElement(object):
def setup(self):
self.store = Store(":memory:")
self.store.set_up()
self.interval = BaseInterval(
"1", 10, 100, name="int1", block_ids=["block1", "block2"], superblock_ids=["sblock1", "sblock1"]
)
self.db_interval = StoreInterval(
interval_id=self.interval.name,
contig=self.interval.contig,
start=self.interval.start,
end=self.interval.end,
strand=self.interval.strand,
)
self.interval_group = [("block2", self.db_interval, "sblock1")]
def test_build_interval(self):
intervals = list(build_interval(self.store, self.interval))
self.store.save()
new_interval = self.store.get("interval", self.interval.name)
assert new_interval.id == self.interval.name
assert new_interval.start == self.interval.start
assert len(intervals) == 2
def test_build_block(self):
superblock_id, new_block = build_block(self.store, self.interval_group)
self.store.save()
db_block = self.store.get("block", self.interval_group[0][0])
assert superblock_id == "sblock1"
assert new_block.id == db_block.id == self.interval_group[0][0]
assert new_block.start == db_block.start == self.interval_group[0][1].start
