API Reference

Loading data from file

Top-level functions for loading data.

load_seq	loads unaligned sequences from file
load_aligned_seqs	loads aligned sequences from file
load_unaligned_seqs	loads unaligned sequences from file
parse.table.load_delimited	basic processing of tabular data
core.table.load_table	return a Table instance from a file containing tabular data.
core.tree.load_tree	Constructor for tree.
core.annotation_db.load_annotations	loads annotations from flatfile into a db

Making cogent3 objects

Constructors from standard Python types.

make_seq
core.alignment.make_aligned_seqs	Initialise an aligned collection of sequences.
core.alignment.make_unaligned_seqs	Initialise an unaligned collection of sequences.
core.table.make_table	make a Table instance
core.tree.make_tree	Initialises a tree.

Getting commonly used types

core.genetic_code.get_code	returns the genetic code
core.moltype.get_moltype	returns the moltype with the matching name attribute
evolve.models.get_model	returns an instance of the named model

Listing builtins

core.genetic_code.available_codes	returns Table listing the available genetic codes
core.moltype.available_moltypes	returns Table listing the available moltypes
evolve.models.available_models	returns Table listing the pre-defined substitution models
app.available_apps	returns Table listing the available apps

Sequences

Biological sequence objects.

core.sequence.Sequence	Holds the standard Sequence object. Immutable.
core.sequence.DnaSequence	Holds the standard DNA sequence.
core.sequence.RnaSequence	Holds the standard RNA sequence.
core.sequence.ProteinSequence	Holds the standard Protein sequence.

Sequence collections & alignments

core.alignment.SequenceCollection	A container of unaligned sequences.
core.alignment.Alignment	A collection of aligned sequences.
core.alignment.Aligned	A single sequence in an alignment.

Sequence storage & views

core.seq_storage.SeqsData	The builtin cogent3 implementation of sequence storage underlying
core.seq_storage.AlignedSeqsData	The builtin cogent3 implementation of aligned sequences storage
core.seqview.SeqView	Provides a view of a sequence with support for slicing operations.
core.seqview.SeqDataView	A view class for SeqsData, providing methods for different
core.seqview.AlignedDataView	A view class for AlignedSeqsData, providing methods for different representations
core.slice_record.SliceRecord	records cumulative slice operations on an object without modifying it

Annotations

core.annotation.Feature	new style annotation, created on demand
core.annotation_db.BasicAnnotationDb	Provides a user table for annotations. This can be merged with
core.annotation_db.GffAnnotationDb	Support for annotations from gff files. Records that span multiple
core.annotation_db.GenbankAnnotationDb	Support for annotations from Genbank files.

Molecular types & alphabets

core.moltype.MolType	MolType handles operations that depend on the sequence type.
core.genetic_code.GeneticCode	Holds codon to amino acid mapping, and vice versa.
core.alphabet.CharAlphabet	representing fundamental monomer character sets.
core.alphabet.KmerAlphabet	k-mer alphabet represents complete non-monomer alphabets
core.alphabet.SenseCodonAlphabet	represents the sense-codons of a GeneticCode
core.alphabet.PhredEncoding	fastq quality score encoding schemes

Tables

core.table.Table	Tabular data. iter operates over rows. Columns are available as an attribute.
core.table.Columns	Collection of columns. iter operates over columns.
parse.table.FilteringParser	A parser for a delimited tabular file that returns records matching a condition.

Trees

core.tree.PhyloNode

Store information about a tree node. Mutable.