cogent3.core.alignment.SequenceCollection

class SequenceCollection(*, seqs_data: SeqsDataABC, moltype: c3_moltype.MolType[Any], info: dict[str, Any] | InfoClass | None = None, source: PathType | None = None, annotation_db: AnnotationDbABC | list[AnnotationDbABC] | None = None, name_map: Mapping[str, str] | None = None, is_reversed: bool = False)

A container of unaligned sequences.

Attributes:

annotation_db

the annotation database for the collection

modified

collection is a modification of underlying storage

name_map

returns mapping of seq names to parent seq names

names

returns the names of the sequences in the collection

num_seqs

the number of sequences in the collection

seqs

iterable of sequences in the collection

storage

the unaligned sequence storage instance of the collection

Methods

add_feature(*[, seqid, parent_id, strand])	add feature on named sequence
add_seqs(seqs, **kwargs)	Returns new collection with additional sequences.
apply_pssm([pssm, path, background, ...])	scores sequences using the specified pssm
copy_annotations(seq_db)	copy annotations into attached annotation db
count_ambiguous_per_seq()	Counts of ambiguous characters per sequence.
count_kmers([k, use_hook])	return kmer counts for each sequence
counts([motif_length, include_ambiguity, ...])	counts of motifs
counts_per_seq([motif_length, ...])	counts of motifs per sequence
degap([storage_backend])	returns collection sequences without gaps or missing characters.
distance_matrix([calc])	Estimated pairwise distance between sequences
dotplot([name1, name2, window, threshold, ...])	make a dotplot between two sequences.
drop_duplicated_seqs()	returns self without duplicated sequences
duplicated_seqs()	returns the names of duplicated sequences
entropy_per_seq([motif_length, ...])	Returns the Shannon entropy per sequence.
from_rich_dict(data)	returns a new instance from a rich dict
get_ambiguous_positions()	Returns dict of seq:{position:char} for ambiguous chars.
get_features(*[, seqid, biotype, name, ...])	yields Feature instances
get_identical_sets([mask_degen])	returns sets of names for sequences that are identical
get_lengths([include_ambiguity, allow_gap])	returns sequence lengths as a dict of {seqid: length}
get_motif_probs([alphabet, ...])	Return a dictionary of motif probs, calculated as the averaged frequency across sequences.
get_seq(seqname[, copy_annotations])	Return a Sequence object for the specified seqname.
get_seq_names_if(f[, negate])	Returns list of names of seqs where f(seq) is True.
get_similar(target, min_similarity, ...)	Returns new SequenceCollection containing sequences similar to target.
get_translation([gc, incomplete_ok, ...])	translate sequences from nucleic acid to protein
has_annotation_db()	returns True if self has annotation db
has_terminal_stop([gc, strict])	Returns True if any sequence has a terminal stop codon.
is_ragged()	rerturns True if sequences are of different lengths
iter_seqs([seq_order])	Iterates over sequences in the collection, in order.
make_feature(*, feature, **kwargs)	create a feature on named sequence, or on the collection itself
pad_seqs([pad_length])	Returns copy in which sequences are padded with the gap character to same length.
probs_per_seq([motif_length, ...])	return frequency array of motifs per sequence
rc()	Returns the reverse complement of all sequences in the collection.
renamed_seqs(renamer)	Returns new collection with renamed sequences.
replace_annotation_db(value[, check])	public interface to assigning the annotation_db
reverse_complement()	Returns the reverse complement of all sequences in the collection.
set_repr_policy([num_seqs, num_pos, ...])	specify policy for repr(self)
strand_symmetry([motif_length])	returns dict of strand symmetry test results per seq
take_seqs(names[, negate, copy_annotations])	Returns new collection containing only specified seqs.
take_seqs_if(f[, negate])	Returns new collection containing seqs where f(seq) is True.
to_dict(-> dict[str, str]  -> dict[str, str])	Return a dictionary of sequences.
to_dna()	returns copy of self as a collection of DNA moltype seqs
to_fasta([block_size])	Return collection in Fasta format.
to_html([name_order, wrap, limit, colors, ...])	returns html with embedded styles for sequence colouring
to_json()	returns json formatted string
to_moltype(moltype)	returns copy of self with changed moltype
to_rich_dict()	returns a json serialisable dict
to_rna()	returns copy of self as a collection of RNA moltype seqs
trim_stop_codons([gc, strict])	Removes any terminal stop codons from the sequences
write(filename[, format_name])	Write the sequences to a file, preserving order of sequences.

Notes

Should be constructed using make_unaligned_seqs().