Gtf

Module providing functions for handling GTF data. More...

Macros
#define	DEFAULT_ATTR_SIZE    64
	How many attributes should be allocated by default.
#define	CORE_FIELD_COUNT   8
	The number of core fields in a GTF line.

Enumerations
enum	gtfFields {   SEQNAME = 0 , SOURCE = 1 , FEATURE = 2 , START = 3 ,   END = 4 , SCORE = 5 , REVERSE = 6 , FRAME = 7 ,   ATTRIBUTES = 8 }
	Enum containing the fields that a GTF line can contain. More...

Functions
GtfDict *	createGTFdict (const occurrence_t *restrict token, PyObject *attr_tp, hashmap_t *restrict attr_keys, hashmap_t *restrict attr_vals)
	Parses a singular GTF line into a Python dict.
bool	validGTFLineToParse (const char *line, size_t len)
	Determines if the provided line is a valid GTF line that can be parsed safely.

Variables
const char *	keywords [CORE_FIELD_COUNT]
	Array containing the keywords of the GTF fields.
const uint8_t	keyword_sizes [CORE_FIELD_COUNT]
	Array containing the sizes of the keywords.
const PyTypeObject *	keyword_types [CORE_FIELD_COUNT]
	Array containing the types of the keywords.

Detailed Description

Module providing functions for handling GTF data.

See also

https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md

Macro Definition Documentation

CORE_FIELD_COUNT

#define CORE_FIELD_COUNT   8

The number of core fields in a GTF line.

This is better than using ATTRIBUTES, as it's more descriptive

DEFAULT_ATTR_SIZE

#define DEFAULT_ATTR_SIZE    64

How many attributes should be allocated by default.

See also

GtfDict

Enumeration Type Documentation

gtfFields

enum gtfFields

Enum containing the fields that a GTF line can contain.

See also

GtfDict

keywords

Enumerator
SEQNAME
SOURCE
FEATURE
START
END
SCORE
REVERSE
FRAME
ATTRIBUTES

Function Documentation

createGTFdict()

GtfDict * createGTFdict	(	const occurrence_t *restrict	token,
		PyObject *	attr_tp,
		hashmap_t *restrict	attr_keys,
		hashmap_t *restrict	attr_vals
	)

Parses a singular GTF line into a Python dict.

Parameters

token	the GTF line to parse. It should contain a minimum of 7 \t, else it will throw an error
attr_tp	a mapping containing the callable to use to convert the attribute values to the correct type, or None
attr_keys	a hashmap containing the keys of the attributes
attr_vals	a hashmap containing the values of the attributes

Returns

a PyObject* pointing to an object of type dict, or NULL on error

See also

occurrence_t

GtfDict

validGTFLineToParse()

bool validGTFLineToParse	(	const char *	line,
		size_t	len
	)

Determines if the provided line is a valid GTF line that can be parsed safely.

A line is considered valid if it doesn't start with a # and contains at least one \t

Parameters

line	the line to check
len	the length of the line

Returns

true or false depending on line validity

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Variable Documentation

keyword_sizes

const uint8_t keyword_sizes[CORE_FIELD_COUNT]

extern

Array containing the sizes of the keywords.

keyword_types

const PyTypeObject* keyword_types[CORE_FIELD_COUNT]

extern

Array containing the types of the keywords.

keywords

const char* keywords[CORE_FIELD_COUNT]

extern

Array containing the keywords of the GTF fields.