FastaBuff.c File Reference

Implementations for the FastaBuff object. More...

#include "FastaBuff.h"
#include <stdbool.h>
#include <stdint.h>
#include <stdio.h>
#include <Python.h>
#include "../common.h"
#include "../formats/fasta.h"
#include "GtfDict.h"

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Functions
static int	FastaBuff_init (FastaBuff *self, PyObject *restrict args, PyObject *restrict kwds)
	Initializes a FastaBuff object.
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 PyObject *	FastaBuff_getItem (FastaBuff *self, Py_ssize_t index)
	Gets a part of the sequence.
static int	FastaBuff_setItem (FastaBuff *self, Py_ssize_t index, PyObject *value)
	Sets a part of the sequence.
static int	FastaBuff_strindex (FastaBuff *self, size_t offset, size_t end, const char *value, size_t len)
	Returns the index of the first occurrence of the specified sequence in this FastaBuff, or -1 if this FastaBuff does not contain the sequence.
static int	FastaBuff_buffindex (FastaBuff *self, size_t offset, size_t end, FastaBuff *restrict other)
	Returns the index of the first occurrence of the specified sequence in this FastaBuff.
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 args)
	Counts the number of occurrences of the specified value in this FastaBuff.
static PyObject *	FastaBuff_dump (FastaBuff *restrict self, PyObject *args)
	Converts the FastaBuff to a bytes object.
static PyObject *	FastaBuff_get_annotated (FastaBuff *restrict self, PyObject *restrict args)
	Returns the annotated sequence.
static PyObject *	FastaBuff_richcompare (FastaBuff *restrict self, PyObject *restrict other, const int op)
	FastaBuff comparison function.
static PyObject *	FastaBuff_getSubscript (FastaBuff *restrict self, PyObject *restrict key)
	Gets a subsequence of the FastaBuff.
static PyObject *	FastaBuff_find (FastaBuff *restrict self, PyObject *restrict args)
	Finds occurrences of the specified sequence in this FastaBuff.
static PyObject *	FastaBuff_iterator_new (FastaBuff *buff, bool reverse)
static PyObject *	FastaBuff_iter (FastaBuff *self)
static PyObject *	FastaBuff_reversed (FastaBuff *self)
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.
static void	FastaBuff_iterator_dealloc (FastaBuff_iterator *self)
static PyObject *	FastaBuff_iterator_iter (FastaBuff_iterator *self)
static PyObject *	FastaBuff_iterator_next (FastaBuff_iterator *self)

Variables
static PyMethodDef	FastaBuffMethods []
	The FastaBuff methods.
static PyMappingMethods	FastaBuffMap
	The FastaBuff mapping methods.
static PySequenceMethods	FastaBuffSeq
	The FastaBuff sequence methods.
PyTypeObject	FastaBuffType
	The Python type definition for the FastaBuff object.
PyTypeObject	FastaBuff_iteratorType

Detailed Description

Implementations for the FastaBuff object.

Function Documentation

FastaBuff_buffindex()

static int FastaBuff_buffindex ( FastaBuff *  self, size_t  offset, size_t  end, FastaBuff *restrict  other  )

static

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

Parameters

self	the FastaBuff to search in
offset	the offset to start searching from
end	the end offset to stop searching at
other	the other FastaBuff to search for

Returns

The index of the first occurrence of the specified sequence, or -1 on error.

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FastaBuff_getItem()

static PyObject * FastaBuff_getItem ( FastaBuff *  self, Py_ssize_t  index  )

static

Gets a part of the sequence.

Parameters

self	the FastaBuff to get the part from
index	the index to get the part from

Returns

the part of the sequence

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FastaBuff_iter()

static PyObject * FastaBuff_iter ( FastaBuff *  self )

static

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FastaBuff_iterator_dealloc()

static void FastaBuff_iterator_dealloc ( FastaBuff_iterator *  self )

static

FastaBuff_iterator_iter()

static PyObject * FastaBuff_iterator_iter ( FastaBuff_iterator *  self )

static

FastaBuff_iterator_new()

static PyObject * FastaBuff_iterator_new ( FastaBuff *  buff, bool  reverse  )

static

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FastaBuff_iterator_next()

static PyObject * FastaBuff_iterator_next ( FastaBuff_iterator *  self )

static

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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_reversed()

static PyObject * FastaBuff_reversed ( FastaBuff *  self )

static

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FastaBuff_strindex()

static int FastaBuff_strindex ( FastaBuff *  self, size_t  offset, size_t  end, const char *  value, size_t  len  )

static

Returns the index of the first occurrence of the specified sequence in this FastaBuff, or -1 if this FastaBuff does not contain the sequence.

Parameters

self	the FastaBuff to search in
offset	the offset to start searching from
end	the end offset to stop searching at
value	substring
len	length of substring

Returns

The index of the first occurrence of the specified sequence, or -1 on error.

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Variable Documentation

FastaBuff_iteratorType

PyTypeObject FastaBuff_iteratorType

Initial value:

= {
    PyVarObject_HEAD_INIT(NULL, 0).tp_name = "eccLib.FastaBuff_iterator",
    .tp_basicsize = sizeof(FastaBuff_iterator),
    .tp_doc =
        PyDoc_STR("An iterator for a buffer for storing a FASTA sequence"),
    .tp_itemsize = 0,
    .tp_flags = Py_TPFLAGS_DEFAULT,
    .tp_new = PyType_GenericNew,
    .tp_iter = (getiterfunc)FastaBuff_iterator_iter,
    .tp_iternext = (iternextfunc)FastaBuff_iterator_next,
    .tp_dealloc = (destructor)FastaBuff_iterator_dealloc}

FastaBuffMap

PyMappingMethods FastaBuffMap

static

Initial value:

= {.mp_subscript =
                                            (binaryfunc)FastaBuff_getSubscript}

The FastaBuff mapping methods.

FastaBuffMethods

PyMethodDef FastaBuffMethods[]

static

Initial value:

= {
    {"dump", (PyCFunction)FastaBuff_dump, METH_NOARGS,
     "Dumps the buffer as bytes"},
    {"index", (PyCFunction)FastaBuff_index, METH_VARARGS,
     "Returns the index of the first occurrence of the specified sequence in "
     "this FastaBuff."},
    {"get_annotated", (PyCFunction)FastaBuff_get_annotated, METH_VARARGS,
     "Returns the annotated sequence based on the GtfDict"},
    {"count", (PyCFunction)FastaBuff_count, METH_VARARGS,
     "Returns the number of occurrences of the specified sequence in this "
     "FastaBuff."},
    {"find", (PyCFunction)FastaBuff_find, METH_VARARGS,
     "Returns the indices of the first occurrence of the specified sequence in "
     "this FastaBuff."},
    {"__reversed__", (PyCFunction)FastaBuff_reversed, METH_NOARGS,
     "Returns the reverse of the sequence"},
    {NULL, NULL, 0, NULL} 
}

The FastaBuff methods.

FastaBuffSeq

PySequenceMethods FastaBuffSeq

static

Initial value:

= {
    .sq_length = (lenfunc)FastaBuff_len,
    .sq_ass_item = (ssizeobjargproc)FastaBuff_setItem,
    .sq_contains = (objobjproc)FastaBuff_contains,
}

The FastaBuff sequence methods.