Molecular types

The MolType object provides services for resolving ambiguities, or providing the correct ambiguity for recoding. It also maintains the mappings between different kinds of alphabets, sequences and alignments.

If your analysis involves handling ambiguous states, or translation via a genetic code, it’s critical to specify the appropriate moltype.

Available molecular types

from cogent3 import available_moltypes

available_moltypes()

Specify a moltype by the Abbreviation (case insensitive).

Abbreviation	Number of states	Moltype
'ab'	2	MolType(('a', 'b'))
'dna'	4	MolType(('T', 'C', 'A', 'G'))
'rna'	4	MolType(('U', 'C', 'A', 'G'))
'protein'	21	MolType(('A', 'C', 'D', 'E', 'F', 'G', ...
'protein_with_stop'	22	MolType(('A', 'C', 'D', 'E', 'F', 'G', ...
'text'	52	MolType(('a', 'b', 'c', 'd', 'e', 'f', ...
'bytes'	256	MolType(('\x00', '\x01', '\x02', '\x03'...

7 rows x 3 columns

For statements that have a moltype argument, use the entry under the “Abbreviation” column. For example:

from cogent3 import load_aligned_seqs

seqs = load_aligned_seqs("data/brca1-bats.fasta", moltype="dna")

Getting a MolType

from cogent3 import get_moltype

dna = get_moltype("dna")
dna

MolType(('T', 'C', 'A', 'G'))

Using a MolType to get ambiguity codes

Just using dna from above.

dna.ambiguities

{'?': ('T', 'C', 'A', 'G', '-'),
 '-': ('-',),
 'N': ('A', 'C', 'T', 'G'),
 'R': ('A', 'G'),
 'Y': ('C', 'T'),
 'W': ('A', 'T'),
 'S': ('C', 'G'),
 'K': ('T', 'G'),
 'M': ('C', 'A'),
 'B': ('C', 'T', 'G'),
 'D': ('A', 'T', 'G'),
 'H': ('A', 'C', 'T'),
 'V': ('A', 'C', 'G'),
 'T': ('T',),
 'C': ('C',),
 'A': ('A',),
 'G': ('G',)}

MolType definition of degenerate codes

dna.degenerates

{'N': ('A', 'C', 'T', 'G'),
 'R': ('A', 'G'),
 'Y': ('C', 'T'),
 'W': ('A', 'T'),
 'S': ('C', 'G'),
 'K': ('T', 'G'),
 'M': ('C', 'A'),
 'B': ('C', 'T', 'G'),
 'D': ('A', 'T', 'G'),
 'H': ('A', 'C', 'T'),
 'V': ('A', 'C', 'G'),
 '?': 'TCAG-'}

Nucleic acid MolType and complementing

dna.complement("AGG")

'TCC'

Making sequences

Use the either the top level cogent3.make_seq function, or the method on the MolType instance.

seq = dna.make_seq("AGGCTT", name="seq1")
seq

	0
seq1	AGGCTT

DnaSequence, length=6

Verify sequences

rna = get_moltype("rna")
rna.is_valid("ACGUACGUACGUACGU")

True

Making a custom MolType

We demonstrate this by customising DNA so it allows . as gaps

from cogent3.core import moltype as mt

DNAgapped = mt.MolType(
    seq_constructor=mt.DnaSequence,
    motifset=mt.IUPAC_DNA_chars,
    ambiguities=mt.IUPAC_DNA_ambiguities,
    complements=mt.IUPAC_DNA_ambiguities_complements,
    pairs=mt.DnaStandardPairs,
    gaps=".",
)
seq = DNAgapped.make_seq("ACG.")
seq

	0
None	ACG.

DnaSequence, length=4

Warning

At present, constructing a custom MolType that overrides a builtin one affects the original (in this instance, the DnaSequence class). All subsequent calls to the original class in the running process that made the change are affected. The below code is resetting this attribute now to allow the rest of the documentation to be executed.

from cogent3 import DNA
from cogent3.core.sequence import DnaSequence

DnaSequence.moltype = DNA