GtfList

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

Data Structures
struct	GtfList
	A list that holds geneDicts. More...

Functions
static int	GtfList_init (GtfList *restrict self, PyObject *args, PyObject *restrict kwds)
	Initializes a new GtfList object.
static PyObject *	GtfList_findHost (GtfList *restrict self, PyObject *restrict gene)
	Finds the host gene of the gene in args assuming this object contains the correct host gene.
static int	GtfList_mp_ass_subscript (GtfList *restrict self, PyObject *restrict key, PyObject *restrict value)
	Wrapper over the default setitem that performs a type check.
static PyObject *	GtfList_append (GtfList *restrict self, PyObject *restrict new)
	Wrapper over list.append that throws a type error if the provided arg is not a GtfDict.
static PyObject *	GtfList_inplace_concat (GtfList *restrict self, PyObject *restrict o)
	concatenates o to self
static PyObject *	GtfList_extend (GtfList *restrict self, PyObject *restrict iterable)
	Custom list extend that does a type check.
static PyObject *	GtfList_insert (GtfList *restrict self, PyObject *restrict args)
	A wrapper over the default list insert that does a type check.
static PyObject *	GtfList_concat (GtfList *restrict self, PyObject *restrict other)
	non discriminatory implementation of add. Does no checks and returns a LIST
static PyObject *	GtfList_str (GtfList *restrict self)
	Generates a complete GTF file.
static PyObject *	GtfList_repr (GtfList *restrict self)
	Generates a representation of the GtfList object.
static PyObject *	GtfList_sq_split (GtfList *restrict self)
	Splits the gene list into a dict of GtfLists with each GtfList having only one seqname.
static PyObject *	GtfList_column (GtfList *restrict self, PyObject *restrict key)
	Gets the values of a column in the GtfList.
static PyObject *	GtfList_find (GtfList *restrict self, PyObject *restrict args, PyObject *restrict kwargs)
	Finds a sequence within the GtfList.

Variables
PyTypeObject	GtfListType
	The Python type definition for the GtfList object.

Detailed Description

All methods and objects related to the GtfList object.

The GtfList object is a list that holds geneDicts. It is used to store the parsed GTF data. It exists to provide type checking and to allow for easy processing method implementation

Function Documentation

GtfList_append()

PyObject * GtfList_append ( GtfList *restrict self, PyObject *restrict new )

static

Wrapper over list.append that throws a type error if the provided arg is not a GtfDict.

Parameters

self
new	the object to append

Returns

None or NULL on error

GtfList_column()

PyObject * GtfList_column ( GtfList *restrict self, PyObject *restrict key )

static

Gets the values of a column in the GtfList.

Parameters

self
key	The name of the column to get

Returns

a list of values

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GtfList_concat()

PyObject * GtfList_concat ( GtfList *restrict self, PyObject *restrict other )

static

non discriminatory implementation of add. Does no checks and returns a LIST

Parameters

self
other	an iterable to be concatenated

Returns

a new list object

GtfList_extend()

PyObject * GtfList_extend ( GtfList *restrict self, PyObject *restrict iterable )

static

Custom list extend that does a type check.

Parameters

self
iterable	the iterable to extend with

Returns

None or NULL on error

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GtfList_find()

PyObject * GtfList_find ( GtfList *restrict self, PyObject *restrict args, PyObject *restrict kwargs )

static

Finds a sequence within the GtfList.

Parameters

self
args	A list of functions to check the objects against
kwargs	A dict of key -> value | function to check the value under the key

Returns

a list of matching objects

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GtfList_findHost()

PyObject * GtfList_findHost ( GtfList *restrict self, PyObject *restrict gene )

static

Finds the host gene of the gene in args assuming this object contains the correct host gene.

Parameters

self
gene	the gene to find the host for

Returns

None or a new GtfDict reference

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GtfList_init()

int GtfList_init ( GtfList *restrict self, PyObject * args, PyObject *restrict kwds )

static

Initializes a new GtfList object.

Parameters

self
args	the arguments tuple, either a tuple of values for a new list, or a tuple with a iterable inside to convert
kwds	must be NULL or else error

GtfList_inplace_concat()

PyObject * GtfList_inplace_concat ( GtfList *restrict self, PyObject *restrict o )

static

concatenates o to self

Parameters

self
o	the object to concatenate to self

Returns

self as a new reference

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GtfList_insert()

PyObject * GtfList_insert ( GtfList *restrict self, PyObject *restrict args )

static

A wrapper over the default list insert that does a type check.

Parameters

self
args	tuple with (index, value)

Returns

None or NULL on error

GtfList_mp_ass_subscript()

int GtfList_mp_ass_subscript ( GtfList *restrict self, PyObject *restrict key, PyObject *restrict value )

static

Wrapper over the default setitem that performs a type check.

Parameters

self
key	int or slice
value	GtfDict or iterable of GtfDicts

Returns

-1 on error

GtfList_repr()

PyObject * GtfList_repr ( GtfList *restrict self )

static

Generates a representation of the GtfList object.

Parameters

self

Returns

a string representation of the object

GtfList_sq_split()

PyObject * GtfList_sq_split ( GtfList *restrict self )

static

Splits the gene list into a dict of GtfLists with each GtfList having only one seqname.

Parameters

self

Returns

A dict seqname->GtfList

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GtfList_str()

PyObject * GtfList_str ( GtfList *restrict self )

static

Generates a complete GTF file.

Parameters

self

Returns

Str PyObject or NULL on error

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Variable Documentation

GtfListType

PyTypeObject GtfListType

extern

The Python type definition for the GtfList object.