valerius.sequences

Classes for the various kinds of Biological sequence.

class valerius.sequences.Sequence(string, label='')[source]

A string sequence of some kind.

Parameters

string (str) – the raw string.

property type

The type of sequence.

Return type

str

property length

The length of the string.

Return type

int

property string

The sequence’s raw string.

Return type

str

property label

The sequence’s descriptive label.

Return type

str

property frequencies

Returns the frequency of each character in the sequence.

Return type

Counter

property codes

Returns the list of multi-letter codes corresponding to this sequence.

Return type

list

class valerius.sequences.PeptideSequence(string, label='')[source]

A sequence of protein residues.

Parameters

string (str) – the raw string.

property codes

Returns the list of multi-letter codes corresponding to this sequence.

Return type

list

property frequencies

Returns the frequency of each character in the sequence.

Return type

Counter

property label

The sequence’s descriptive label.

Return type

str

property length

The length of the string.

Return type

int

property string

The sequence’s raw string.

Return type

str

property type

The type of sequence.

Return type

str

class valerius.sequences.NucleotideSequence(string, label='')[source]

A sequence of nucleotide bases.

Parameters

string (str) – the raw string.

property gc_content

Returns the proportion of G and C residues in the sequence.

Return type

float

property codes

Returns the list of multi-letter codes corresponding to this sequence.

Return type

list

property frequencies

Returns the frequency of each character in the sequence.

Return type

Counter

property label

The sequence’s descriptive label.

Return type

str

property length

The length of the string.

Return type

int

property string

The sequence’s raw string.

Return type

str

property type

The type of sequence.

Return type

str

class valerius.sequences.DnaSequence(string, label='')[source]

A sequence of DNA nucleotide bases.

Parameters

string (str) – the raw string.

property codes

Returns the list of multi-letter codes corresponding to this sequence.

Return type

list

property frequencies

Returns the frequency of each character in the sequence.

Return type

Counter

property gc_content

Returns the proportion of G and C residues in the sequence.

Return type

float

property label

The sequence’s descriptive label.

Return type

str

property length

The length of the string.

Return type

int

property string

The sequence’s raw string.

Return type

str

property type

The type of sequence.

Return type

str

class valerius.sequences.RnaSequence(string, label='')[source]

A sequence of RNA nucleotide bases.

Parameters

string (str) – the raw string.

property codes

Returns the list of multi-letter codes corresponding to this sequence.

Return type

list

property frequencies

Returns the frequency of each character in the sequence.

Return type

Counter

property gc_content

Returns the proportion of G and C residues in the sequence.

Return type

float

property label

The sequence’s descriptive label.

Return type

str

property length

The length of the string.

Return type

int

property string

The sequence’s raw string.

Return type

str

property type

The type of sequence.

Return type

str