Sequence Location (`pyncbitk.objects.seqloc`)#

Locations on a biological sequence.

This module contains classes that are used to describe a location on a BioSeq.

class pyncbitk.objects.seqloc.SeqLoc(Serial)#

An abstract base class for defining a location in a BioSeq.

classmethod __new__(*args, **kwargs)#

__reduce__()#: Helper for pickle.

class pyncbitk.objects.seqloc.NullLoc(SeqLoc)#

A region of unknown length for which no data exists.

classmethod __new__(*args, **kwargs)#

__reduce__()#: Helper for pickle.

class pyncbitk.objects.seqloc.EmptySeqLoc(SeqLoc)#

A gap of unknown size inside an alignment.

classmethod __new__(*args, **kwargs)#

__reduce__()#: Helper for pickle.

class pyncbitk.objects.seqloc.WholeSeqLoc(SeqLoc)#

A reference to an entire BioSeq.

classmethod __new__(*args, **kwargs)#

__init__(id)#

Create a new location referencing the given sequence.

Parameters:: sequence_id (SeqId) – The identifier of the sequence being referenced.

__reduce__()#: Helper for pickle.

__repr__()#: Return repr(self).

sequence_id#

The identifier of the sequence.

Type:: SeqId

class pyncbitk.objects.seqloc.SeqIntervalLoc(SeqLoc)#

A reference to an interval on a BioSeq.

An interval is a single continuous region of defined length on a BioSeq.

classmethod __new__(*args, **kwargs)#

__init__(*args, **kwargs)#

__reduce__()#: Helper for pickle.

__repr__()#: Return repr(self).

sequence_id#

The identifier of the sequence.

Type:: SeqId

start#

The beginining of the sequence interval.

Type:: int

stop#

The end of the sequence interval (inclusive).

Type:: int

class pyncbitk.objects.seqloc.PackedSeqLoc(SeqLoc)#

A reference to a series of intervals on a BioSeq.

classmethod __new__(*args, **kwargs)#

__reduce__()#: Helper for pickle.

class pyncbitk.objects.seqloc.PointLoc(SeqLoc)#

A reference to a single point on a BioSeq.

classmethod __new__(*args, **kwargs)#

__reduce__()#: Helper for pickle.

class pyncbitk.objects.seqloc.PackedPointsLoc(SeqLoc)#

A reference to a series of points on a BioSeq.

classmethod __new__(*args, **kwargs)#

__reduce__()#: Helper for pickle.

class pyncbitk.objects.seqloc.MixLoc(SeqLoc)#

An arbitrarily complex location.

classmethod __new__(*args, **kwargs)#

__reduce__()#: Helper for pickle.

class pyncbitk.objects.seqloc.EquivalentLoc(SeqLoc)#

A set of equivalent locations.

classmethod __new__(*args, **kwargs)#

__reduce__()#: Helper for pickle.

class pyncbitk.objects.seqloc.BondLoc(SeqLoc)#

A chemical bond between two residues.

classmethod __new__(*args, **kwargs)#

__reduce__()#: Helper for pickle.

class pyncbitk.objects.seqloc.FeatureLoc(SeqLoc)#

A location indirectly referenced through a feature.

classmethod __new__(*args, **kwargs)#

__reduce__()#: Helper for pickle.

Sequence Location (pyncbitk.objects.seqloc)#

Sequence Location (`pyncbitk.objects.seqloc`)#