Sequence container used throughout ConKit
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
¶str – A unique identifier
seq_len
¶int – The protein sequence length
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: | |
---|---|
Returns: | Tuple containing two |
Return 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
instances
Parameters: | |
---|---|
Returns: | Tuple containing two |
Return 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