cogent3.core.alignment.Alignment#

class Alignment(seqs_data: AlignedSeqsDataABC, slice_record: SliceRecord | None = None, **kwargs: Any)#

A collection of aligned sequences.

Attributes:

annotation_db: the annotation database for the collection
array_positions: Returns a numpy array of positions, axis 0 is alignment positions columns in order corresponding to names.
array_seqs: Returns a numpy array of sequences, axis 0 is seqs in order
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
positions
seqs: iterable of sequences in the collection
storage: the aligned sequence storage instance of the collection

Methods

`add_feature`(*[, seqid, parent_id, strand, ...])	add feature on named sequence, or on the alignment itself
`add_seqs`(seqs, **kwargs)	Returns new collection with additional sequences.
`alignment_quality`([app_name])	Computes the alignment quality using the indicated app
`apply_scaled_gaps`(other[, aa_to_codon])	applies gaps in self to ungapped sequences
`coevolution`([stat, segments, drawable, ...])	performs pairwise coevolution measurement
`copy`([copy_annotations])	creates new instance, only mutable attributes are copied
`copy_annotations`(seq_db)	copy annotations into attached annotation db
`count_ambiguous_per_seq`()	Return the counts of ambiguous characters per sequence as a DictArray.
`count_gaps_per_pos`([include_ambiguity])	return counts of gaps per position as a DictArray
`count_gaps_per_seq`([induced_by, unique, ...])	return counts of gaps per sequence as a DictArray
`counts`([motif_length, include_ambiguity, ...])	counts of motifs
`counts_per_pos`([motif_length, ...])	return MotifCountsArray of counts per position
`counts_per_seq`([motif_length, ...])	counts of non-overlapping motifs per sequence
`deepcopy`(**kwargs)	returns deep copy of self
`degap`([storage_backend])	returns collection sequences without gaps or missing characters.
`distance_matrix`([calc, drop_invalid, parallel])	Returns pairwise distances 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_pos`([motif_length, ...])	returns shannon entropy per position
`entropy_per_seq`([motif_length, ...])	Returns the Shannon entropy per sequence.
`filtered`(predicate[, motif_length, ...])	The alignment positions where predicate(column) is true.
`get_ambiguous_positions`()	Returns dict of seq:{position:char} for ambiguous chars.
`get_degapped_relative_to`(name)	Remove all columns with gaps in sequence with given name.
`get_drawable`(*[, biotype, width, vertical, ...])	make a figure from sequence features
`get_drawables`(*[, biotype])	returns a dict of drawables, keyed by type
`get_features`(*[, seqid, biotype, name, ...])	yields Feature instances
`get_gap_array`([include_ambiguity])	returns bool array with gap state True, False otherwise
`get_gapped_seq`(seqname[, recode_gaps])	Return a gapped Sequence object for the specified seqname.
`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_position_indices`(f[, negate])	Returns list of column indices for which f(col) is True.
`get_projected_feature`(*, seqid, feature)	returns an alignment feature projected onto the seqid sequence
`get_projected_features`(, seqid, *kwargs)	projects all features from other sequences onto seqid
`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.
`information_plot`([width, height, window, ...])	plot information per position
`is_ragged`()	by definition False for an Alignment
`iter_positions`([pos_order])	Iterates over positions in the alignment, in order.
`iter_seqs`([seq_order])	Iterates over sequences in the collection, in order.
`iupac_consensus`([allow_gap])	Returns string containing IUPAC consensus sequence of the alignment.
`majority_consensus`()	Returns consensus sequence containing most frequent item at each position.
`make_feature`(*, feature[, on_alignment])	create a feature on named sequence, or on the alignment itself
`matching_ref`(ref_name, gap_fraction, gap_run)	Returns new alignment with seqs well aligned with a reference.
`no_degenerates`([motif_length, allow_gap])	returns new alignment without degenerate characters
`omit_bad_seqs`([quantile])	Returns new alignment without sequences with a number of uniquely introduced gaps exceeding quantile
`omit_gap_pos`([allowed_gap_frac, motif_length])	Returns new alignment where all cols (motifs) have <= allowed_gap_frac gaps.
`pad_seqs`([pad_length])	Returns copy in which sequences are padded with the gap character to same length.
`probs_per_pos`([motif_length, ...])	returns MotifFreqsArray per position
`probs_per_seq`([motif_length, ...])	return frequency array of motifs per sequence
`quick_tree`([calc, drop_invalid, parallel, ...])	Returns a phylogenetic tree.
`rc`()	Returns the reverse complement of all sequences in the alignment.
`renamed_seqs`(renamer)	Returns new alignment 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.
`sample`(*, n, with_replacement, motif_length, ...)	Returns random sample of positions from self, e.g. to bootstrap.
`seqlogo`([width, height, wrap, vspace, colours])	returns Drawable sequence logo using mutual information
`sliding_windows`(window, step[, start, end])	Generator yielding new alignments of given length and interval.
`strand_symmetry`([motif_length])	returns dict of strand symmetry test results per ungapped seq
`take_positions`(cols[, negate])	Returns new Alignment containing only specified positions.
`take_positions_if`(f[, negate])	Returns new Alignment containing cols where f(col) is True.
`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_phylip`()	Return collection in PHYLIP format and mapping to sequence ids
`to_pretty`([name_order, wrap])	returns a string representation of the alignment in pretty print format
`to_rich_dict`()	returns a json serialisable dict
`to_rna`()	returns copy of self as a collection of RNA moltype seqs
`variable_positions`([include_gap_motif, ...])	Return a list of variable position indexes.
`with_masked_annotations`(biotypes[, ...])	returns an alignment with regions replaced by mask_char
`write`(filename[, format_name])	Write the sequences to a file, preserving order of sequences.

from_rich_dict
gapped_by_map
trim_stop_codons

Notes

Should be constructed using make_aligned_seqs().