Note about dtype

By default, almost every operation in dinopy will return results in the Python type bytes. However, most of these operations accept the keyword argument dtype which may be set to any of the following values:

• bytes

  Return the ascii-encoded bases as python bytes, e.g. b'ACGT' (which is basically the same as [65, 67, 71, 84]). This is the default.

• bytearray

  A mutable version of bytes.

• str

  Return the result as utf-8 string (capital letters), e.g. "ACGT".

• basenumbers

  Maps A → 0, C → 1, G → 2, T → 3, N → 4, ..., e.g. [0, 1, 2, 3] (or, more correctly, as bytes: b'\x00\x01\x02\x03').

Sometimes, as is the case with dinopy.processors.qgrams, you can also supply the keyword argument ‘encoding’ with either of the following values:

• two_bit

  Encodes the result as a long integer. If characters other than "ACGT" are encountered, they will be randomly replaced according to the usual IUPAC mapping (see IUPAC mapping for details).

• four_bit

  Basically the same as two_bit, but does not need to replace characters other than "ACGT", as each character of the IUPAC specification can be encoded using exactly 4 bit. For example, "ACGTM" translates to 0b 0001 0010 0100 1000 0011.

Note

All of these types can be accessed like dinopy.two_bit or dinopy.definitions.two_bit.

You can use the functions dinopy.conversion.encode and dinopy.conversion.decode to manually convert qgrams to and from 2bit / 4bit encoding.

IUPAC mapping

DNA sequences may contain characters other than A, C, G or T, namely: N, U, R, Y, M, K, W, S, B, D, H and V. If such a character is encountered while encoding a sequence to a single long integer two-bit representation, they will get replaced randomly (uniform) according to the following mapping:

Character	Replace
N	A	C	G	T
U				T
R	A		G
Y		C		T
M	A	C
K			G	T
W	A			T
S		C	G
B		C	G	T
D	A		G	T
H	A	C		T
V	A	C	G