# Bio.CAPS package

## Module contents

Cleaved amplified polymorphic sequence (CAPS) markers.

A CAPS marker is a location a DifferentialCutsite as described below and a set of primers that can be used to visualize this. More information can be found in the paper Konieczny and Ausubel (1993) (PMID 8106085).

class Bio.CAPS.DifferentialCutsite(**kwds)

  Bases: `object`

  Differential enzyme cutsite in an alignment.

  A differential cutsite is a location in an alignment where an enzyme cuts at least one sequence and also cannot cut at least one other sequence.

  Members:

    - start - Where it lives in the alignment.

    - enzyme - The enzyme that causes this.

    - cuts_in - A list of sequences (as indexes into the alignment) the enzyme cuts in.

    - blocked_in - A list of sequences (as indexes into the alignment) the enzyme is blocked in.

  __init__(**kwds)

    Initialize a DifferentialCutsite.

    Each member (as listed in the class description) should be included as a keyword.

  __annotate_func__ = None
  __annotations_cache__ = {}
  __firstlineno__ = 20
  __static_attributes__ = ('blocked_in', 'cuts_in', 'enzyme', 'start')

exception Bio.CAPS.AlignmentHasDifferentLengthsError

  Bases: `Exception`

  Exception where sequences in alignment have different lengths.

  __firstlineno__ = 48
  __static_attributes__ = ()

class Bio.CAPS.CAPSMap(alignment, enzymes=None)

  Bases: `object`

  A map of an alignment showing all possible dcuts.

  Members:

    - alignment - The alignment that is mapped.

    - dcuts - A list of possible CAPS markers in the form of DifferentialCutsites.

  __init__(alignment, enzymes=None)

    Initialize the CAPSMap.

    Required:

      - alignment - The alignment to be mapped.

    Optional:

      - enzymes - List of enzymes to be used to create the map. Defaults to an empty list.

  __annotate_func__ = None
  __annotations_cache__ = {}
  __firstlineno__ = 52
  __static_attributes__ = ('alignment', 'dcuts', 'enzymes', 'length', 'sequences', 'size')

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