conkit.core.sequence module¶

Sequence container used throughout ConKit

class Sequence(id, seq)[source]¶

Bases: conkit.core._entity._Entity

A sequence template to store all associated information

Examples

>>> from conkit.core import Sequence
>>> sequence_entry = Sequence("example", "ABCDEF")
>>> print(sequence_entry)
Sequence(id="example" seq="ABCDEF" seqlen=6)

Attributes

`id`	The ID of the selected entity
`remark`	The `Sequence`-specific remarks
`seq`	The protein sequence as `str`
`seq_len`	The protein sequence length

Methods

`add`(entity)	Add a child to the `Entity`
`align_global`(other[, id_chars, nonid_chars, …])	Generate a global alignment between two `Sequence` instances
`align_local`(other[, id_chars, nonid_chars, …])	Generate a local alignment between two `Sequence` instances
`copy`()	Create a shallow copy of `Entity`
`deepcopy`()	Create a deep copy of `Entity`
`remove`(id)	Remove a child

align_global(other, id_chars=2, nonid_chars=1, gap_open_pen=-0.5, gap_ext_pen=-0.1, inplace=False)[source]¶

Generate a global alignment between two Sequence instances

Parameters:

Parameters:	other : `Sequence` id_chars : int, optional nonid_chars : int, optional gap_open_pen : float, optional gap_ext_pen : float, optional inplace : bool, optional Replace the saved order of residues [default: False]
Returns:	obj The reference to the `Sequence`, regardless of inplace obj The reference to the `Sequence`, regardless of inplace

other : Sequence

id_chars : int, optional

nonid_chars : int, optional

gap_open_pen : float, optional

gap_ext_pen : float, optional

inplace : bool, optional

Replace the saved order of residues [default: False]

Returns:

obj

The reference to the Sequence, regardless of inplace

obj

The reference to the Sequence, regardless of inplace

align_local(other, id_chars=2, nonid_chars=1, gap_open_pen=-0.5, gap_ext_pen=-0.1, inplace=False)[source]¶

Generate a local alignment between two Sequence instances

Parameters:

Parameters:	other : `Sequence` id_chars : int, optional nonid_chars : int, optional gap_open_pen : float, optional gap_ext_pen : float, optional inplace : bool, optional Replace the saved order of residues [default: False]
Returns:	obj The reference to the `Sequence`, regardless of inplace obj The reference to the `Sequence`, regardless of inplace

other : Sequence

id_chars : int, optional

nonid_chars : int, optional

gap_open_pen : float, optional

gap_ext_pen : float, optional

inplace : bool, optional

Replace the saved order of residues [default: False]

Returns:

obj

The reference to the Sequence, regardless of inplace

obj

The reference to the Sequence, regardless of inplace

remark¶: The Sequence-specific remarks

seq¶: The protein sequence as str

seq_ascii¶: The protein sequence as ASCII-encoded str

seq_len¶: The protein sequence length