reader

A module providing a C "base classes" for FastaReader, GtfReader and GtfFile, FastaFile. More...

Data Structures
struct	reader
	Reader base struct. More...
struct	file
	File base struct. More...
struct	line_out
	A simple that hold a string, and potentially it's Python parent object. More...

Functions
void	free_reader (struct reader *self)
	Free the reader object.
PyObject *	file_enter (struct file *self, PyObject *args)
	enter method for file objects
PyObject *	file_exit (struct file *self, PyObject *args, PyObject *kwds)
	exit method for file objects
bool	initialize_reader (const struct file *self, struct reader *reader)
	Initialize the reader object based on the file object.
line_out	next_line (struct reader *restrict self, bool(*valid)(const char *, size_t))
	Fetches the next line from the reader object.

Detailed Description

A module providing a C "base classes" for FastaReader, GtfReader and GtfFile, FastaFile.

For maintainability and to avoid duplicating code, plenty of similar functionality was generalized from GtfReader into this module. Through the magic of pointers, basic polymorphism is achieved. For example: both FastaReader and GtfReader are derived from the reader struct. They both have that struct as the first field, meaning functions taking in reader* as arguments can use them.

Function Documentation

file_enter()

PyObject * file_enter	(	struct file *	self,
		PyObject *	args
	)

enter method for file objects

This function opens the file and ensures the file is ready for reader creation.

Parameters

self	the file object
args	arguments passed to enter

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file_exit()

PyObject * file_exit	(	struct file *	self,
		PyObject *	args,
		PyObject *	kwds
	)

exit method for file objects

Parameters

self	the file object
args	arguments passed to exit
kwds	keyword arguments passed to exit

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free_reader()

void free_reader

(

struct reader *

self

)

Free the reader object.

Parameters

self	the reader object

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initialize_reader()

bool initialize_reader	(	const struct file *	self,
		struct reader *	reader
	)

Initialize the reader object based on the file object.

This function does all the sanity checks, resets the FILE object, and initializes the reader object

Parameters

self	the file object
reader	the allocated reader object

Returns

true on success, false on failure

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next_line()

line_out next_line	(	struct reader *restrict	self,
		bool(*)(const char *, size_t)	valid
	)

Fetches the next line from the reader object.

This function returns a line_out structure containing the next line from the reader object. Unfortunately, the line may contain the '
' character. Use Py_XDECREF to release the returned structure.

Parameters

self	the reader object

Returns

the next line from the reader object

Warning

the returned line token buffer may be owned by the reader object

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