cogent3.core.sequence.DnaSequence#

Holds the standard DNA sequence.

Attributes:

annotation_db: the annotation database for the collection
annotation_offset: The offset between annotation coordinates and sequence coordinates.
info
moltype
name

Methods

`add_feature`(*, biotype, name, spans[, ...])	add a feature to annotation_db
`annotate_matches_to`(pattern, biotype, name)	Adds an annotation at sequence positions matching pattern.
`can_match`(other)	Returns True if every pos in self could match same pos in other.
`can_mispair`(other)	Returns True if any position in self could mispair with other.
`can_pair`(other)	Returns True if self and other could pair.
`complement`()	Returns complement of self, using data from MolType.
`copy`([exclude_annotations, sliced])	returns a copy of self
`copy_annotations`(seq_db)	copy annotations into attached annotation db
`count`(item)	count() delegates to self._seq.
`count_ambiguous`()	Returns the number of ambiguous characters in the sequence.
`count_degenerate`()	Counts the degenerate bases in the specified sequence.
`count_gaps`()	Counts the gaps in the specified sequence.
`count_kmers`([k, use_hook])	return array of counts of all possible kmers of length k
`count_variants`()	Counts number of possible sequences matching the sequence, given any ambiguous characters in the sequence.
`counts`([motif_length, include_ambiguity, ...])	returns dict of counts of motifs
`degap`()	Deletes all gap characters from sequence.
`diff`(other)	Returns number of differences between self and other.
`disambiguate`([method])	Returns a non-degenerate sequence from a degenerate one.
`distance`(other[, function])	Returns distance between self and other using function(i,j).
`frac_diff`(other)	Returns fraction of positions where self and other differ.
`frac_diff_gaps`(other)	Returns frac.
`frac_diff_non_gaps`(other)	Returns fraction of non-gap positions where self differs from other.
`frac_same`(other)	Returns fraction of positions where self and other are the same.
`frac_same_gaps`(other)	Returns fraction of positions where self and other share gap states.
`frac_same_non_gaps`(other)	Returns fraction of non-gap positions where self matches other.
`frac_similar`(other, similar_pairs)	Returns fraction of positions where self[i] is similar to other[i].
`from_rich_dict`(data)	create a Sequence object from a rich dict
`gap_indices`()	Returns array of the indices of all gaps in the sequence
`gap_vector`()	Returns vector of True or False according to which pos are gaps or missing.
`get_drawable`(*[, biotype, width, vertical])	make a figure from sequence features
`get_drawables`(*[, biotype])	returns a dict of drawables, keyed by type
`get_features`(*[, biotype, name, start, ...])	yields Feature instances
`get_in_motif_size`([motif_length, warn])	returns sequence as list of non-overlapping motifs
`get_kmers`(k[, strict])	return all overlapping k-mers
`get_name`()	Return the sequence name -- should just use name instead.
`get_translation`([gc, incomplete_ok, ...])	translate to amino acid sequence
`get_type`()	Return the sequence type as moltype label.
`has_annotation_db`()	returns True if self has annotation db
`has_terminal_stop`([gc, strict])	Return True if the sequence has a terminal stop codon.
`is_annotated`([biotype])	returns True if sequence parent name has any annotations
`is_degenerate`()	Returns True if sequence contains degenerate characters.
`is_gapped`()	Returns True if sequence contains gaps.
`is_strict`()	Returns True if sequence contains only monomers.
`is_valid`()	Returns True if sequence contains no items absent from alphabet.
`iter_kmers`(k[, strict])	generates all overlapping k-mers.
`make_feature`(feature, *args)	return an Feature instance from feature data
`matrix_distance`(other, matrix)	Returns distance between self and other using a score matrix.
`must_pair`(other)	Returns True if all positions in self must pair with other.
`mw`([method, delta])	Returns the molecular weight of (one strand of) the sequence.
`parent_coordinates`([apply_offset])	returns seqid, start, stop, strand of this sequence on its parent
`parse_out_gaps`()	returns Map corresponding to gap locations and ungapped Sequence
`rc`()	Converts a nucleic acid sequence to its reverse complement.
`replace_annotation_db`(value[, check])	public interface to assigning the annotation_db
`resolved_ambiguities`()	Returns a list of sets of strings.
`reverse_complement`()	Converts a nucleic acid sequence to its reverse complement.
`sample`(*, n, with_replacement, motif_length, ...)	Returns random sample of positions from self, e.g. to bootstrap.
`shuffle`()	returns a randomized copy of the Sequence object
`sliding_windows`(window, step[, start, end])	Generator function that yield new sequence objects of a given length at a given interval.
`strand_symmetry`([motif_length])	returns G-test for strand symmetry
`strip_bad`()	Removes any symbols not in the alphabet.
`strip_bad_and_gaps`()	Removes any symbols not in the alphabet, and any gaps.
`strip_degenerate`()	Removes degenerate bases by stripping them out of the sequence.
`to_array`([apply_transforms])	returns the numpy array
`to_dna`()	Returns copy of self as DNA.
`to_fasta`([make_seqlabel, block_size])	Return string of self in FASTA format, no trailing newline
`to_html`([wrap, limit, colors, font_size, ...])	returns html with embedded styles for sequence colouring
`to_json`()	returns a json formatted string
`to_moltype`(moltype)	returns copy of self with moltype seq
`to_phylip`([name_len, label_len])	Return string of self in one line for PHYLIP, no newline.
`to_rich_dict`([exclude_annotations])	returns {'name': name, 'seq': sequence, 'moltype': moltype.label}
`to_rna`()	Returns copy of self as RNA.
`trim_stop_codon`([gc, strict])	Removes a terminal stop codon from the sequence
`with_masked_annotations`(biotypes[, ...])	returns a sequence with annot_types regions replaced by mask_char if shadow is False, otherwise all other regions are masked.
`with_termini_unknown`()	Returns copy of sequence with terminal gaps remapped as missing.
`write`(filename[, format_name])	Write the sequence to a file.

gapped_by_map
gapped_by_map_motif_iter
gapped_by_map_segment_iter
to_dict