skbio.sequence.NucleotideMixin

class skbio.sequence.NucleotideMixin

Mixin for adding funtionality for working with sequences of nucleotides.

This is an abstract base class (ABC) that cannot be instantiated.

See also

DNA

RNA

Attributes

complement_map

Return mapping of nucleotide characters to their complements.

Methods

complement([reverse])	Return the complement of the nucleotide sequence.
gc_content()	Calculate the relative frequency of G's and C's in the sequence.
gc_frequency([relative])	Calculate frequency of G's and C's in the sequence.
is_reverse_complement(other)	Determine if a sequence is the reverse complement of this sequence.
reverse_complement()	Return the reverse complement of the nucleotide sequence.

Special methods (inherited)

__eq__(value, /)	Return self==value.
__ge__(value, /)	Return self>=value.
__getstate__(/)	Helper for pickle.
__gt__(value, /)	Return self>value.
__hash__(/)	Return hash(self).
__le__(value, /)	Return self<=value.
__lt__(value, /)	Return self<value.
__ne__(value, /)	Return self!=value.
__str__(/)	Return str(self).

Details

complement_map

Return mapping of nucleotide characters to their complements.

Returns:

dict

Mapping of each character to its complement.

Notes

Complements cannot be defined for a generic nucleotide sequence because the complement of A is ambiguous. Thanks, nature…