Working setup

extractor-module.cc

+#include <Python.h>
+
+#include "extractor-core/include/extractor.h"
+
+#include <cstdlib>
+#include <cstdio>
+#include <cstring>
+
+#include <vector>
+
+
+static PyObject*
+extractor_extract_dna(PyObject*, PyObject* args)
+{
+    char* reference;
+    char* sample;
+
+    if (!PyArg_ParseTuple(args, "ss", &reference, &sample))
+    {
+        return NULL;
+    } // if
+
+    size_t const reference_length = strlen(reference);
+    size_t const sample_length = strlen(sample);
+
+    std::vector<mutalyzer::Variant> const variants = mutalyzer::extract_dna(reference, reference_length, sample, sample_length);
+
+    PyObject* result = PyList_New(0);
+    if (result == NULL)
+    {
+        PyErr_SetString(PyExc_MemoryError, "Could not allocate memory for PyList_New");
+        return NULL;
+    } // if
+
+    for (std::vector<mutalyzer::Variant>::const_iterator it = variants.begin(); it != variants.end(); ++it)
+    {
+        PyObject* item = Py_BuildValue("{s:i, s:i, s:i, s:i, s:i, s:i, s:i}",
+                                       "reference_start", it->reference_start,
+                                       "reference_end", it->reference_end,
+                                       "sample_start", it->sample_start,
+                                       "sample_end", it->sample_end,
+                                       "type", it->type,
+                                       "transposition_start", it->transposition_start,
+                                       "transposition_end", it->transposition_end);
+        if (item == NULL)
+        {
+            PyErr_SetString(PyExc_MemoryError, "Could not allocate memory for Py_BuildValue");
+            return NULL;
+        } // if
+        if (PyList_Append(result, item) != 0)
+        {
+            Py_DECREF(item);
+            PyErr_SetString(PyExc_MemoryError, "Could not allocate memory for PyList_Append");
+            return NULL;
+        } // if
+    } // for
+    return result;
+} // extractor_extract
+
+
+static PyMethodDef ExtractorMethods[] =
+{
+    {"extract_dna", extractor_extract_dna, METH_VARARGS, "Run the extract function."},
+
+    {NULL, NULL, 0, NULL}  // sentinel
+}; // ExtractorMethods
+
+
+static struct PyModuleDef extractormodule =
+{
+    PyModuleDef_HEAD_INIT,
+    "description-extractor",
+    "HGVS Variant Description Extractor",
+    -1,
+    ExtractorMethods
+}; // extractormodule
+
+
+PyMODINIT_FUNC
+PyInit_extractor(void)
+{
+    return PyModule_Create(&extractormodule);
+} // PyInit_extractor
+
+
+int
+main(int, char* argv[])
+{
+    wchar_t* const program = Py_DecodeLocale(argv[0], NULL);
+    if (program == NULL)
+    {
+        fprintf(stderr, "Fatal error: cannot decode argv[0]\n");
+        return EXIT_FAILURE;
+    } // if
+
+    PyImport_AppendInittab("description-extractor", PyInit_extractor);
+
+    Py_SetProgramName(program);
+
+    Py_Initialize();
+
+    PyMem_RawFree(program);
+
+    return EXIT_SUCCESS;
+} // main

setup.py

+from setuptools import setup, Extension
+
+from setuptools.command.build_ext import build_ext
+import subprocess
+
+class git_clone_external(build_ext):
+    def run(self):
+        subprocess.check_call(['git', 'clone', 'https://github.com/mutalyzer/extractor-core.git'])
+        build_ext.run(self)
+
+
+extractor = Extension('description-extractor', sources = ['extractor-module.cc',
+                                                          'extractor-core/src/extractor.cc'])
+
+setup(name = 'description-extractor',
+      version = '3.0',
+      cmdclass = {'build_ext': git_clone_external},
+      description = 'This is the extractor package',
+      ext_modules = [extractor]
+)