k1a Namespace Reference

Classes
class	StrIter
	String iterator. More...
class	StrIterCat
	Line iterator from file. More...
struct	PyStrIterCat
class	StrIterInter
	Intermediate string iterator. More...
struct	PyStrIterInter

Typedefs
typedef std::string(*	transformF) (std::string)

Functions
PyObject *	k1a_system (PyObject *self, PyObject *args)
PyObject *	k1a_test (PyObject *self, PyObject *args)
PyObject *	k1a_str_split (PyObject *self, PyObject *args)
	Splits a string up into multiple pieces, respecting quotation marks. More...
PyObject *	k1a_str_alpha_numeric (PyObject *self, PyObject *args)
	Gets rid of special characters and only retain alpha numeric characters. More...
PyObject *	k1a_str_kmers (PyObject *self, PyObject *args)
	Returns all k-mers for the given string. More...
PyObject *	k1a_str_has_number (PyObject *self, PyObject *args)
	Returns whether the string has any numeric characters inside them. More...
PyObject *	PyStrIterCat_new (std::string fileName)
	Creates a new PyStrIterCat object. More...
PyObject *	PyStrIterCat_new (PyTypeObject *type, PyObject *args, PyObject *kwargs)
PyObject *	PyStrIterCat_conjugate (PyStrIterCat *self, PyObject *Py_UNUSED(ignored))
PyObject *	PyStrIterInter_new (StrIter *og, transformF f)
void	log_clear ()
PyObject *	k1a_log_clear (PyObject *self, PyObject *args)
std::string	demangle (const char *name)
	Demangles C++ signatures. More...
template<class T >
void	log_print (T s)
template<class T >
void	log_println (T s)

Variables
PyMethodDef	K1aMethods []
struct PyModuleDef	k1amodule
PyMethodDef	PyStrIterCat_methods []
PyTypeObject	PyStrIterCat_Type
PyTypeObject	PyStrIterInter_Type
bool	debug = false

Typedef Documentation

transformF

typedef std::string(* k1a::transformF) (std::string)

Definition at line 13 of file StrIter.h.

Function Documentation

demangle()

std::string k1a::demangle

(

const char *

name

)

Demangles C++ signatures.

Parameters

name

Returns

std::string

Definition at line 39 of file utils.cpp.

                                     {
    int status = -4;  // some arbitrary value to eliminate the compiler warning
 
    // enable c++11 by passing the flag -std=c++11 to g++
    std::unique_ptr<char, void (*)(void *)> res{
        abi::__cxa_demangle(name, NULL, NULL, &status),
        std::free};
 
    return (status == 0) ? res.get() : name;
}

k1a_log_clear()

PyObject * k1a::k1a_log_clear	(	PyObject *	self,
		PyObject *	args
	)

Definition at line 23 of file utils.cpp.

                                                        {
    log_clear();
    Py_RETURN_NONE;
}

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k1a_str_alpha_numeric()

PyObject* k1a::k1a_str_alpha_numeric	(	PyObject *	self,
		PyObject *	args
	)

Gets rid of special characters and only retain alpha numeric characters.

Example:

# returns "abg 8 86"
k1a.str_alpha_numeric("abg$%^8,;86")

Definition at line 92 of file funcs.cpp.

                                                                {
    char *_str, *str;
    if (!PyArg_ParseTuple(args, "s", &_str)) return NULL;
    str = (char *)malloc((strlen(_str) + 1) * sizeof(char));
    int i = 0, j = 0;
    bool stillSpecial = false;
 
    while (_str[i] != NULL) {
        unsigned int a = _str[i];
        if ((65 <= a && a <= 90) || (97 <= a && a <= 122) || (48 <= a && a <= 57)) {  // legit characters
            str[j] = a;
            j++;
            stillSpecial = false;
        } else {
            if (!stillSpecial) {
                str[j] = ' ';
                j++;
            }
            stillSpecial = true;
        }
        i++;
    }
    str[j] = '\0';
    auto res = PyUnicode_FromString(str);
    free(str);
    return res;
}

k1a_str_has_number()

PyObject* k1a::k1a_str_has_number	(	PyObject *	self,
		PyObject *	args
	)

Returns whether the string has any numeric characters inside them.

Example:

# returns True
k1a.str_has_number("gh365")
# returns False
k1a.str_has_number("ghj")

Definition at line 161 of file funcs.cpp.

                                                             {
    char *str;
    if (!PyArg_ParseTuple(args, "s", &str)) return NULL;
    int i = 0;
    while (str[i] != NULL) {
        unsigned int a = str[i];
        if (48 <= a && a <= 57) {
            Py_INCREF(Py_True);
            return Py_True;
        }
        i++;
    }
    Py_INCREF(Py_False);
    return Py_False;
}

k1a_str_kmers()

PyObject* k1a::k1a_str_kmers	(	PyObject *	self,
		PyObject *	args
	)

Returns all k-mers for the given string.

Example:

# returns ['012', '123', '234', '345', '456']
k1a.str_kmers("0123456", 3)

Definition at line 130 of file funcs.cpp.

                                                        {
    char *str;
    int k;
    if (!PyArg_ParseTuple(args, "si", &str, &k)) return NULL;
    PyObject *plist = PyList_New(0);
 
    bool inBlock = false;
    int n = strlen(str);
    if (n < k) return plist;
 
    for (int i = 0; i < n - (k - 1); i++) {
        char tmp = str[i + k];
        str[i + k] = '\0';
        PyList_Append(plist, PyUnicode_FromString(str + i));
        str[i + k] = tmp;
    }
    return plist;
}

k1a_str_split()

PyObject* k1a::k1a_str_split	(	PyObject *	self,
		PyObject *	args
	)

Splits a string up into multiple pieces, respecting quotation marks.

Example:

# returns ['ab', "c'd.e'f"]
k1a.str_split("ab.c'd.e'f", ".")

Definition at line 52 of file funcs.cpp.

                                                        {
    char *_str, *_delim, *str, *begin;
    if (!PyArg_ParseTuple(args, "ss", &_str, &_delim)) return NULL;
    char delim = _delim[0], quoteChar = '"';
 
    begin = str = (char *)malloc((strlen(_str) + 1) * sizeof(char));
    strcpy(str, _str);
    PyObject *plist = PyList_New(0);
 
    int i = 0;
    bool inBlock = false;
 
    while (str[i] != NULL) {
        char a = str[i];
        if (a == delim && !inBlock) {
            str[i] = NULL;
            PyList_Append(plist, PyUnicode_FromString(begin));
            begin = str + (i + 1);
        } else if (!inBlock && (a == '"' || a == '\'')) {  // new block
            inBlock = true;
            quoteChar = a;
        } else if (inBlock && a == quoteChar)
            inBlock = false;  // exiting block
        i++;
    }
    PyList_Append(plist, PyUnicode_FromString(begin));
    free(str);
    return plist;
}

k1a_system()

PyObject* k1a::k1a_system	(	PyObject *	self,
		PyObject *	args
	)

Definition at line 17 of file funcs.cpp.

                                                     {
    const char *command;
    int sts;
 
    if (!PyArg_ParseTuple(args, "s", &command)) return NULL;
    sts = system(command);
    if (sts < 0) {
        // TODO: add exception string
        return NULL;
    }
    return PyLong_FromLong(sts);
}

k1a_test()

PyObject* k1a::k1a_test	(	PyObject *	self,
		PyObject *	args
	)

Definition at line 30 of file funcs.cpp.

                                                   {
    const char *str;
    if (!PyArg_ParseTuple(args, "s", &str)) return NULL;
    const std::string a = str;
    auto b = (PyStrIterCat *)PyStrIterCat_new(a);
    auto f1 = [](std::string x) { return x + " |end"; };
    auto f2 = [](std::string x) { return "begin| " + x; };
    return b->val->transform(std::vector<transformF>{f1, f2}, true)->pyObj;
    //  return PyUnicode_FromString("def");
    //  return PyUnicode_FromString((a + "end").c_str());
}

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log_clear()

void k1a::log_clear

(

)

Definition at line 16 of file utils.cpp.

                 {
    std::ofstream f;
    f.open("/home/kelvin/repos/labs/k1a/logs.txt");
    f << "";
    f.close();
}

log_print()

template<class T >

void k1a::log_print

(

T

s

)

Definition at line 13 of file utils.h.

                    {
    std::ofstream f;
    f.open("/home/kelvin/repos/labs/k1a/logs.txt", std::ios_base::app);
    f << s;
    f.close();
}

log_println()

template<class T >

void k1a::log_println

(

T

s

)

Definition at line 21 of file utils.h.

                      {
    log_print(s);
    log_print("\n");
}

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PyStrIterCat_conjugate()

PyObject* k1a::PyStrIterCat_conjugate	(	PyStrIterCat *	self,
		PyObject *	Py_UNUSEDignored
	)

Definition at line 56 of file StrIterCat.cpp.

                                                                                   {
    return PyUnicode_FromString("str_iter_conjugate");
};

PyStrIterCat_new() [1/2]

PyObject * k1a::PyStrIterCat_new	(	PyTypeObject *	type,
		PyObject *	args,
		PyObject *	kwargs
	)

Definition at line 44 of file StrIterCat.cpp.

                                                                                 {
    PyStrIterCat *return_value = PyObject_New(PyStrIterCat, type);
    char *fileName;
    PyArg_ParseTuple(args, "s", &fileName);
    return PyStrIterCat_new(std::string(fileName));
}

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PyStrIterCat_new() [2/2]

PyObject * k1a::PyStrIterCat_new

(

std::string

fileName

)

Creates a new PyStrIterCat object.

Parameters

fileName

Returns

PyObject*

Definition at line 37 of file StrIterCat.cpp.

                                               {
    if (debug) log_println("PyStrIterCat_new");
    PyStrIterCat *res = PyObject_New(PyStrIterCat, &PyStrIterCat_Type);
    res->val = new StrIterCat((PyObject *)res, fileName);
    return (PyObject *)res;
}

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PyStrIterInter_new()

PyObject * k1a::PyStrIterInter_new	(	StrIter *	og,
		transformF	f
	)

Definition at line 18 of file StrIterInter.cpp.

                                                        {
    PyStrIterInter *pyObj = PyObject_New(PyStrIterInter, &PyStrIterInter_Type);
    char *fileName;
    if (debug) log_println("PyStrIterInter_new");
    pyObj->val = new StrIterInter((PyObject *)pyObj, og, f);
    return (PyObject *)pyObj;
}

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Variable Documentation

debug

bool k1a::debug = false

Definition at line 14 of file utils.cpp.

K1aMethods

PyMethodDef k1a::K1aMethods

Initial value:

= {
    {"system", k1a_system, METH_VARARGS, "Execute a shell command."},
    {"test", k1a_test, METH_VARARGS,
     "Test function for developing the library"},
    {"clear", k1a_log_clear, METH_VARARGS, "Clear logs"},
    {"str_split", k1a_str_split, METH_VARARGS,
     "str_split(s, ch). Splits string into multiple fragments using a delimiter, respecting quotes."
     "\n\nExample: k1a.str_split(\"'ab'cdb3\", \"b\") == [\"'ab'cd\", \"3\"]"},
    {"str_alpha_numeric", k1a_str_alpha_numeric, METH_VARARGS, "str_alpha_numeric(s). Replaces characters that are not alpha numeric with white spaces. \n\nExample: str_alpha_numeric(\"4,.53-45ag\") == \"4 53 45ag\""},
    {"str_kmers", k1a_str_kmers, METH_VARARGS, "str_kmers(s, k). Gets a string's k-mers. \n\nExample: k1a.str_kmers(\"abcde\", 2) == ['ab', 'bc', 'cd', 'de']"},
    {"str_has_number", k1a_str_has_number, METH_VARARGS, "str_has_number(s). Returns whether the string has any numeric characters inside them."},
    {NULL, NULL, 0, NULL} 
}

Definition at line 177 of file funcs.cpp.

k1amodule

struct PyModuleDef k1a::k1amodule

Initial value:

= {
    PyModuleDef_HEAD_INIT, "k1a", 
    NULL,                         
    -1,                           
    K1aMethods}

Definition at line 177 of file funcs.cpp.

PyStrIterCat_methods

PyMethodDef k1a::PyStrIterCat_methods[]

Initial value:

= {
    {"conjugate", (PyCFunction)PyStrIterCat_conjugate, METH_NOARGS, "conjugate docs"},
    {NULL, NULL}}

Definition at line 60 of file StrIterCat.cpp.

PyStrIterCat_Type

PyTypeObject k1a::PyStrIterCat_Type

Definition at line 64 of file StrIterCat.cpp.

PyStrIterInter_Type

PyTypeObject k1a::PyStrIterInter_Type

Definition at line 39 of file StrIterInter.cpp.