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_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)