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)
-
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
instancesParameters: Returns: Tuple containing two
Sequence
instances, regardless of inplaceReturn type:
-
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
instancesParameters: Returns: Tuple containing two
Sequence
instances, regardless of inplaceReturn type:
-
remark
The
Sequence
-specific remarks
-
seq
The protein sequence as
str
-
seq_encoded
¶ The protein sequence encoded by numbers
-
seq_len
The protein sequence length
-