MultiSequence

class MultiSequence(sequences, name=None, mode=None, metadata=None, aligned=False, **kwargs)

Class responsible for handling multiple sequences.

Constructor for MultiSequence

Parameters

• sequences (Any) – Anything that can be parsed as multiple sequences.

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

• mode (Optional[str]) – Mode of the sequences. All sequences must have same mode/type. Otherwise error will be raised

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

• aligned (bool) – True if sequences are aligned. Default is False

• kwargs (Any) – Compatibility

Attributes

count	Total number of sequences.
index	Indices of the internals sequences.
is_alignment	Is mutli-sequence is aligned or not.
is_buckled	Is mulit-sequence instance is buckled or not.
metadata	Instance metadata.
mode	Mode/type of the sequences.
name	Name of the instance.
sequences	List of individual sequence instances.
skbio_mode	The skbio mode of the sequence.

Methods

buckle_for_alignment()	Buckle individual sequences for alignment.
copy()	Copy current instance.
from_buckled(sequences, buckled_pack, **kwargs)	Factory method to create MultiSequence using packed metadata from buckling.
get_consensus([indices])	If sequence are aligned, estimate consensus sequence from the MSA
get_iter([method])	Get generator for the idividual sequences.
get_string_as(**kwargs)	Get string of all sequences.
get_subset([indices])	Get subset of the mutli-sequence instance.
restore_buckle(buckled_pack)	Restore the buckled MultiSequence instance.
to_skbio_msa([indices])	Convert to skbio TabularMSA instance.
write(file[, mode])	Write the sequence data into the file.