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