Molecular types#

Note

Alpha Release of the New MolType API

We are pleased to announce an alpha release of our new MolType API. This version can be accessed by specifying the argument new_type=True in the get_moltype() function.

Please be aware that this alpha release has not been fully integrated with the library. Users are encouraged to explore its capabilities but should proceed with caution!

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
np.str_('ab')	2	MolType(('a', 'b'))
np.str_('dna')	4	MolType(('T', 'C', 'A', 'G'))
np.str_('rna')	4	MolType(('U', 'C', 'A', 'G'))
np.str_('protein')	21	MolType(('A', 'C', 'D', 'E', 'F', 'G', ...
np.str_('protein_with_stop')	22	MolType(('A', 'C', 'D', 'E', 'F', 'G', ...
np.str_('text')	52	MolType(('a', 'b', 'c', 'd', 'e', 'f', ...
np.str_('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

Molecular types#

Available molecular types#

Getting a MolType#

Using a MolType to get ambiguity codes#

MolType definition of degenerate codes#

Nucleic acid MolType and complementing#