GtfList.c File Reference

Contains the implementation of the GtfList object. More...

#include "GtfList.h"
#include <stdbool.h>
#include <stdlib.h>
#include <Python.h>
#include "../../common.h"
#include "../../formats/gtf.h"
#include "../GtfDict/GtfDict.h"
#include "GtfListViews.h"
#include "longobject.h"

Include dependency graph for GtfList.c:

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.
static PyObject *	GtfList_get_contigs (GtfList *restrict self)
PyObject *	GtfList_new (Py_ssize_t len)
	Creates a new GtfList object.

Variables
static char	newline = '\n'
static PyMethodDef	GtfList_methods []
	The methods of the GtfList object.
static PySequenceMethods	GtfListSq
	The sequence methods of the GtfList object.
static PyMappingMethods	GtfListMap
	The mapping methods of the GtfList object.
PyTypeObject	GtfListType
	The Python type definition for the GtfList object.

Detailed Description

Contains the implementation of the GtfList object.

Function Documentation

GtfList_get_contigs()

static PyObject * GtfList_get_contigs ( GtfList *restrict self )

static

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GtfList_new()

PyObject * GtfList_new

(

Py_ssize_t

len

)

Creates a new GtfList object.

Parameters

len	the length of the list

Returns

a new GtfList object

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Variable Documentation

GtfList_methods

PyMethodDef GtfList_methods[]

static

Initial value:

= {
    {"find_closest_bound", (PyCFunction)GtfList_findHost, METH_O,
     "Returns None or the approximate host gene of the provided GtfDict"},
    {"append", (PyCFunction)GtfList_append, METH_O,
     "Appends the provided element to the GtfList"},
    {"extend", (PyCFunction)GtfList_extend, METH_O,
     "Extends the gene list with the provided iterable"},
    {"insert", (PyCFunction)GtfList_insert, METH_VARARGS,
     "Inserts the provided object at the provided position"},
    {"sq_split", (PyCFunction)GtfList_sq_split, METH_NOARGS,
     "Splits this gene list by the seqnames"},
    {"find", (PyCFunction)GtfList_find, METH_VARARGS | METH_KEYWORDS,
     "Splits this gene list by the seqnames"},
    {"column", (PyCFunction)GtfList_column, METH_O,
     "Returns a list of the values of the provided key"},
    {"get_contigs", (PyCFunction)GtfList_get_contigs, METH_NOARGS,
     "Returns a list of the contig ranges of the genes"},
    {NULL, NULL, 0, NULL} 
}

The methods of the GtfList object.

GtfListMap

PyMappingMethods GtfListMap

static

Initial value:

= {
    .mp_ass_subscript = (objobjargproc)GtfList_mp_ass_subscript}

The mapping methods of the GtfList object.

GtfListSq

PySequenceMethods GtfListSq

static

Initial value:

= {.sq_inplace_concat =
                                          (binaryfunc)GtfList_inplace_concat,
                                      .sq_concat = (binaryfunc)GtfList_concat}

The sequence methods of the GtfList object.

newline

char newline = '\n'

static