bx.intervals package

Subpackages

• bx.intervals.operations package
  • Submodules
    • bx.intervals.operations.base_coverage module
    • bx.intervals.operations.complement module
    • bx.intervals.operations.concat module
    • bx.intervals.operations.coverage module
    • bx.intervals.operations.find_clusters module
    • bx.intervals.operations.intersect module
    • bx.intervals.operations.join module
    • bx.intervals.operations.merge module
    • bx.intervals.operations.quicksect module
    • bx.intervals.operations.subtract module
  • Module contents
    • bits_clear_in_range()
    • bits_set_in_range()

Submodules

• bx.intervals.cluster module
  • ClusterTree
    • ClusterTree.getlines()
    • ClusterTree.getregions()
    • ClusterTree.insert()
• bx.intervals.cluster_tests module
  • TestCluster
    • TestCluster.insertpairs()
    • TestCluster.setUp()
    • TestCluster.test_another()
    • TestCluster.test_distance()
    • TestCluster.test_duplicates()
    • TestCluster.test_easymerge()
    • TestCluster.test_hardmerge()
    • TestCluster.test_large_sorted()
    • TestCluster.test_larger()
    • TestCluster.test_merge_case()
    • TestCluster.test_merge_left_right()
    • TestCluster.test_minregions()
    • TestCluster.test_none()
    • TestCluster.test_startbeforeend()
    • TestCluster.test_trivial()
• bx.intervals.intersection module
  • Intersecter
  • Interval
    • Interval.chrom
    • Interval.end
    • Interval.start
    • Interval.strand
    • Interval.value
  • IntervalNode
    • IntervalNode.end
    • IntervalNode.find()
    • IntervalNode.insert()
    • IntervalNode.intersect()
    • IntervalNode.interval
    • IntervalNode.left()
    • IntervalNode.left_node
    • IntervalNode.right()
    • IntervalNode.right_node
    • IntervalNode.root_node
    • IntervalNode.start
    • IntervalNode.traverse()
  • IntervalTree
    • IntervalTree.add()
    • IntervalTree.add_interval()
    • IntervalTree.after()
    • IntervalTree.after_interval()
    • IntervalTree.before()
    • IntervalTree.before_interval()
    • IntervalTree.downstream_of_interval()
    • IntervalTree.find()
    • IntervalTree.insert()
    • IntervalTree.insert_interval()
    • IntervalTree.traverse()
    • IntervalTree.upstream_of_interval()
• bx.intervals.intersection_tests module
  • IntervalTreeTest
    • IntervalTreeTest.setUp()
    • IntervalTreeTest.test_empty()
    • IntervalTreeTest.test_find()
    • IntervalTreeTest.test_public_interval()
    • IntervalTreeTest.test_traverse()
  • LotsaTestCase
    • LotsaTestCase.setUp()
    • LotsaTestCase.test_count()
    • LotsaTestCase.test_find()
    • LotsaTestCase.test_max_dist()
  • NeighborTestCase
    • NeighborTestCase.setUp()
    • NeighborTestCase.test_left()
    • NeighborTestCase.test_right()
    • NeighborTestCase.test_toomany()
  • UpDownStreamTestCase
    • UpDownStreamTestCase.setUp()
    • UpDownStreamTestCase.test_downstream()
    • UpDownStreamTestCase.test_n()
    • UpDownStreamTestCase.test_upstream()
• bx.intervals.io module
  • BitsetSafeReaderWrapper
  • FieldFormatError
  • GenomicInterval
    • GenomicInterval.copy()
  • GenomicIntervalReader
    • GenomicIntervalReader.binned_bitsets()
    • GenomicIntervalReader.parse_row()
  • MissingFieldError
  • NiceReaderWrapper
    • NiceReaderWrapper.iterwrapper()
  • StrandFormatError
• bx.intervals.random_intervals module
  • MaxtriesException
  • overwrite_start_end()
  • throw_random_bits()
  • throw_random_gap_list()
  • throw_random_intervals()
  • throw_random_list()
  • throw_random_private()

Module contents

Tools and data structures for working with genomic intervals (or sets of regions on a line in general) efficiently.