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