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.

exception Bio.CAPS.AlignmentHasDifferentLengthsError

Bases: Exception

Exception where sequences in alignment have different lengths.

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.