Nucleotide

class Nucleotide(sequence, name=None, metadata=None, mode='DNA', **kwargs)

Class that represent single nucleotide sequence.

Constructor for the Nucleotide.

Parameters

• sequence (Union[skbio.sequence._grammared_sequence.GrammaredSequence, str]) – Sequence data

• name (Optional[str]) – Name of the sequence instance

• metadata (Optional[dict]) – Metadata of the sequence instance

• mode (str) – Sequence type/mode of the new instance # TODO: Validation currently passes “protein” fix it.

• kwargs (Any) – Compatibility

Attributes

is_buckled	Is sequence instance is buckled or not.
length	Length of the sequence.
metadata	Sequence instance metadata.
mode	Sequence instance mode/type.
name	Name of the sequence instance.
skbio	The skbio representation of the sequence as skbio.sequence.GrammaredSequence
skbio_mode	The skbio mode of the sequence.
text	Sequence as string.

Methods

buckle_by_uid(uid)	Buckle sequences based on unique identifier uid.
complement()	Return the sequence complement as new instance.
copy()	Copy of the current instance.
get_string_as([format])	Get string of the sequence.
read(file[, name, metadata, mode])	Factory class that reads the sequence data.
restore_buckle(buckled_pack)	Restore the buckle using packed metadata buckle_pack
unbuckle_uid()	Retrieve unique identifier assigned during buckling.
write(file[, format])	Write sequence data to the file.