FastaBuff

All methods and objects related to the FastaBuff object. More...

Data Structures
struct	FastaBuff
	A buffer that holds packed uint4 FASTA data. More...

Functions
static FastaBuff *	FastaBuff_new (PyTypeObject *type, PyObject *args, PyObject *kwargs)
	Allocates a new FastaBuff object.
static int	FastaBuff_init (FastaBuff *self, PyObject *restrict args, PyObject *restrict kwds)
	Initializes a FastaBuff object. Equivalent to the constructor in Python.
static Py_ssize_t	FastaBuff_len (FastaBuff *self)
	Returns the length of the FastaBuff.
static PyObject *	FastaBuff_str (FastaBuff *self)
	Converts the FastaBuff to a string.
static int	FastaBuff_setItem (FastaBuff *self, Py_ssize_t index, PyObject *value)
	Sets a part of the sequence.
static int	FastaBuff_contains (FastaBuff *restrict self, PyObject *restrict value)
	Checks if the FastaBuff contains the specified value.
static PyObject *	FastaBuff_index (FastaBuff *restrict self, PyObject *restrict args)
	Returns the index of the first occurrence of the specified value in this FastaBuff.
static PyObject *	FastaBuff_count (FastaBuff *restrict self, PyObject *restrict value)
	Counts the number of occurrences of the specified value in this FastaBuff.
static PyObject *	FastaBuff_dump (FastaBuff *restrict self)
	Converts the FastaBuff to a bytes object.
static PyObject *	FastaBuff_get_annotated (FastaBuff *restrict self, PyObject *restrict first)
	Returns the annotated sequence.
static PyObject *	FastaBuff_richcompare (FastaBuff *restrict self, PyObject *restrict other, const int op)
	FastaBuff comparison function.
static PyObject *	FastaBuff_find (FastaBuff *restrict self, PyObject *restrict firstArg)
	Finds occurrences of the specified sequence in this FastaBuff.
static void	FastaBuff_dealloc (FastaBuff *self)
	Deallocates the FastaBuff.
FastaBuff *	FastaBuff_New (uint8_t *restrict buff, size_t buffSize, size_t buffLen, bool RNA)
	Creates a new FastaBuff object.
PyObject *	FastaBuff_getSubscript (FastaBuff *restrict self, PyObject *restrict key)
	Gets a subsequence of the FastaBuff.
uint8_t	FastaBuff_getItem (FastaBuff *self, Py_ssize_t index)
	Gets an item from the FastaBuff.

Variables
PyTypeObject	FastaBuffType
	The Python type definition for the FastaBuff object.

Detailed Description

All methods and objects related to the FastaBuff object.

The FastaBuff object is a memory efficient buffer for FASTA data. It stores the data in a packed format, with each byte containing two 4 bit values. This allows for a 50% reduction in memory usage compared to a regular byte array. The object also provides methods for easy manipulation of the data.

Function Documentation

FastaBuff_contains()

static int FastaBuff_contains ( FastaBuff *restrict  self, PyObject *restrict  value  )

static

Checks if the FastaBuff contains the specified value.

Parameters

self	the FastaBuff to search in
value	the value to search for

Returns

1 if the FastaBuff contains the value, 0 if it does not, -1 on error

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FastaBuff_count()

static PyObject * FastaBuff_count ( FastaBuff *restrict  self, PyObject *restrict  value  )

static

Counts the number of occurrences of the specified value in this FastaBuff.

Parameters

self	the FastaBuff to search in
value	the value to search for

Returns

the number of occurrences of the specified value

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FastaBuff_dealloc()

static void FastaBuff_dealloc ( FastaBuff *  self )

static

Deallocates the FastaBuff.

Parameters

self	the FastaBuff to deallocate

FastaBuff_dump()

static PyObject * FastaBuff_dump ( FastaBuff *restrict  self )

static

Converts the FastaBuff to a bytes object.

Parameters

self	the FastaBuff to convert

Returns

the bytes representation of the FastaBuff

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FastaBuff_find()

static PyObject * FastaBuff_find ( FastaBuff *restrict  self, PyObject *restrict  firstArg  )

static

Finds occurrences of the specified sequence in this FastaBuff.

Parameters

self	the FastaBuff to search in
firstArg	the sequence to search for

Returns

a list of the indices of the first occurrence of the specified sequence in this FastaBuff.

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FastaBuff_get_annotated()

static PyObject * FastaBuff_get_annotated ( FastaBuff *restrict  self, PyObject *restrict  first  )

static

Returns the annotated sequence.

Parameters

self	the FastaBuff to get the annotated sequence from
first	the GtfDict or mapping to get the annotated sequence with

Returns

the annotated sequence

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FastaBuff_getItem()

uint8_t FastaBuff_getItem	(	FastaBuff *	self,
		Py_ssize_t	index
	)

Gets an item from the FastaBuff.

Parameters

self	the FastaBuff to get the item from
index	the index of the item to get

Returns

the item

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FastaBuff_getSubscript()

PyObject * FastaBuff_getSubscript	(	FastaBuff *restrict	self,
		PyObject *restrict	key
	)

Gets a subsequence of the FastaBuff.

Parameters

self	the FastaBuff to get the subsequence from
key	the key to get the subsequence with

Returns

the subsequence

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FastaBuff_index()

static PyObject * FastaBuff_index ( FastaBuff *restrict  self, PyObject *restrict  args  )

static

Returns the index of the first occurrence of the specified value in this FastaBuff.

Parameters

self	the FastaBuff to search in
args	the arguments to search for

Returns

the index of the first occurrence of the specified value, or -1 on error

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FastaBuff_init()

static int FastaBuff_init ( FastaBuff *  self, PyObject *restrict  args, PyObject *restrict  kwds  )

static

Initializes a FastaBuff object. Equivalent to the constructor in Python.

Either loads a valid buffer, from a bytes object, or parses a string from the provided string or file, into a buffer.

Parameters

self	the FastaBuff to initialize
args	positional arguments
kwds	the keyword arguments

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FastaBuff_len()

static Py_ssize_t FastaBuff_len ( FastaBuff *  self )

static

Returns the length of the FastaBuff.

Parameters

self	the FastaBuff to get the length of

Returns

the length of the FastaBuff

FastaBuff_new()

static FastaBuff * FastaBuff_new ( PyTypeObject *  type, PyObject *  args, PyObject *  kwargs  )

static

Allocates a new FastaBuff object.

Used as the allocator by Python for FastaBuff, initializes the object, ensuring all the fields are valid, but does not actually initialize the object.

Parameters

type	the type of the object to allocate
args	the arguments to initialize the FastaBuff with
kwargs	the keyword arguments to initialize the FastaBuff with. Should always be NULL

Returns

a new FastaBuff object, or NULL if allocation fails

Warning

Does not allocate the buffer

FastaBuff_New()

FastaBuff * FastaBuff_New	(	uint8_t *restrict	buff,
		size_t	buffSize,
		size_t	buffLen,
		bool	RNA
	)

Creates a new FastaBuff object.

Parameters

buff	the buffer to use, this will be owned by the FastaBuff object
buffSize	the size of the buffer
buffLen	the length of the sequence
RNA	if true, T will be converted to U

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FastaBuff_richcompare()

static PyObject * FastaBuff_richcompare ( FastaBuff *restrict  self, PyObject *restrict  other, const int  op  )

static

FastaBuff comparison function.

Parameters

self	the FastaBuff to compare
other	the other object to compare
op	the operation to perform

Returns

the result of the comparison

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FastaBuff_setItem()

static int FastaBuff_setItem ( FastaBuff *  self, Py_ssize_t  index, PyObject *  value  )

static

Sets a part of the sequence.

Parameters

self	the FastaBuff to set the part in
index	the index to set the part at
value	the value to set

Returns

0 on success, -1 on error

FastaBuff_str()

static PyObject * FastaBuff_str ( FastaBuff *  self )

static

Converts the FastaBuff to a string.

Parameters

self	the FastaBuff to convert

Returns

the string representation of the FastaBuff

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Variable Documentation

FastaBuffType

PyTypeObject FastaBuffType

extern

The Python type definition for the FastaBuff object.