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)

id¶

A unique identifier

Type:	str

remark¶

The Sequence-specific remarks

Type:	list

seq¶

The protein sequence as str

Type:	str

seq_len¶

The protein sequence length

Type:	int

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:	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:	Tuple containing two `Sequence` instances, regardless of inplace
Return type:	tuple

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:	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:	Tuple containing two `Sequence` instances, regardless of inplace
Return type:	tuple

remark: The Sequence-specific remarks

seq: The protein sequence as str

seq_ascii¶: The protein sequence as ASCII-encoded str

seq_encoded¶: The protein sequence encoded by numbers

seq_len: The protein sequence length