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 args)
	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 args)
	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 args)
	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 args, PyObject *restrict kwargs)
	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()

static PyObject * GtfList_append ( GtfList *restrict  self, PyObject *restrict  args  )

static

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

Parameters

self
args	standard python arg tuple

Returns

None or NULL on error

GtfList_column()

static PyObject * GtfList_column ( GtfList *restrict  self, PyObject *restrict  args, PyObject *restrict  kwargs  )

static

Gets the values of a column in the GtfList.

Parameters

self
args	tuple with a single str
kwargs	optional pad argument

Returns

a list of values

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GtfList_concat()

static 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()

static PyObject * GtfList_extend ( GtfList *restrict  self, PyObject *restrict  args  )

static

Custom list extend that does a type check.

Parameters

self
args	tuple with a single iterable

Returns

None or NULL on error

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GtfList_find()

static 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()

static PyObject * GtfList_findHost ( GtfList *restrict  self, PyObject *restrict  args  )

static

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

Parameters

self
args	standard python argument tuple

Returns

None or a new GtfDict reference

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GtfList_init()

static 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()

static 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()

static 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()

static 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()

static 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()

static 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()

static 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.