{"id":206,"date":"2011-05-26T20:02:57","date_gmt":"2011-05-27T04:02:57","guid":{"rendered":"http:\/\/zhanxw.com\/blog\/?p=206"},"modified":"2011-05-26T20:03:26","modified_gmt":"2011-05-27T04:03:26","slug":"%e5%a6%82%e4%bd%95%e5%9c%a8python%e4%b8%ad%e8%b0%83%e7%94%a8cc%e4%bb%a3%e7%a0%81","status":"publish","type":"post","link":"https:\/\/zhanxw.com\/blog\/2011\/05\/%e5%a6%82%e4%bd%95%e5%9c%a8python%e4%b8%ad%e8%b0%83%e7%94%a8cc%e4%bb%a3%e7%a0%81\/","title":{"rendered":"\u5982\u4f55\u5728Python\u4e2d\u8c03\u7528C\/C++\u4ee3\u7801"},"content":{"rendered":"

\u5982\u4f55\u5728Python\u4e2d\u8c03\u7528C\/C++\u4ee3\u7801
\nHow to mix C\/C++ code in Python<\/p>\n

\u672c\u6587\u4ecb\u7ecd\u4e00\u79cd\u624b\u52a8\u7684\u3001\u7b80\u5355\u7684\u5728Python\u4e2d\u4f7f\u7528C\/C++\u4ee3\u7801\u7684\u65b9\u5f0f\u3002\u8fd9\u4e2a\u65b9\u6cd5\u4e3b\u8981\u4f7f\u7528\u4e86ctypes\u6a21\u5757\u3002\u5176\u4ed6\u7684\u6df7\u5408Python\uff0cC\/C++\u7f16\u7a0b\u7684\u65b9\u6cd5\u8fd8\u6709Swig<\/a> \u548c Boost.Python<\/a>\u3002\u524d\u4e00\u79cd\u65b9\u6cd5\u9700\u8981\u5199\u4e00\u4e2a\u63a5\u53e3\u6587\u4ef6\uff08interface\uff09\uff0c\u800c\u540e\u4e00\u79cd\u9700\u8981\u4f7f\u7528\u5e9e\u5927\u3001\u6df1\u5965\u7684boost\u7c7b\u5e93\uff0c\u540e\u4e24\u8005\u9002\u5408\u53ef\u80fd\u9002\u5408\u66f4\u590d\u6742\u7684\u60c5\u51b5\uff0c\u8fd9\u91cc\u53ea\u4ecb\u7ecd\u7b2c\u4e00\u79cd\u65b9\u6cd5\u3002<\/p>\n

\u6df7\u5408C\/C++\u4ee3\u7801\u9700\u8981\u8fd9\u51e0\u6b65\uff1a
\n1. \u5305\u88c5\u63a5\u53e3 C\/C++ wrap functions up
\n2. \u6253\u5305\u6210\u5171\u4eab\u5e93 Compiling C\/C++ code and pack it to shared library
\n3. Python\u4e2d\u5bfc\u5165\u5171\u4eab\u5e93 Python imports shared library<\/p>\n

\u5148\u4ecb\u7ecd\u4e00\u4e0b\u5317\u4eac\uff0c\u8fd9\u91cc\u6211\u7684C++\u7c7bGenomeSequence\u4f7f\u7528\u4e86\u6a21\u677f\uff08Template\uff09\u548cMemorymap\uff0c\u8fd9\u662f\u4e00\u4e2a\u8bbf\u95ee\u57fa\u56e0\u5e8f\u5217\u7684\u7c7b\uff0c\u6bd4\u5982\u5982\u679c\u4e00\u4e2a\u751f\u7269\u5e8f\u5217\u662fGAGTTTTATCGCTTCCATGACGCAGAAGTTAACACT… \u6211\u4eec\u7684\u7c7b\u662fgs\uff0c\u90a3\u4e48gs[0] = ‘G’, gs[1]=’A’ …. \u6458\u5f55\u76f8\u5173\u7684\u51fd\u6570\u5982\u4e0b\uff1a<\/p>\n

\r\nclass GenomeSequence : public genomeSequenceArray\r\n{\r\npublic:\r\n    \/\/\/ Simple constructor - no implicit file open\r\n    GenomeSequence();\r\n    \/\/\/ set the reference name that will be used in open()\r\n    \/\/\/ \\param referenceFilename the name of the reference fasta file to open\r\n    \/\/\/ \\return false for success, true otherwise\r\n    \/\/\/\r\n    \/\/\/ \\sa open()\r\n    bool setReferenceName(std::string referenceFilename);\r\n    \/\/\/ return the number of bases represented in this reference\r\n    \/\/\/ \\return count of bases\r\n    genomeIndex_t   getNumberBases() const\r\n    {\r\n        return getElementCount();\r\n    }\r\n    inline char operator[](genomeIndex_t index) const\r\n    {\r\n        uint8_t val;\r\n        if (index < getNumberBases())\r\n        {\r\n            if ((index&1)==0)\r\n            {\r\n                val = ((uint8_t *) data)[index>>1] & 0xf;\r\n            }\r\n            else\r\n            {\r\n                val = (((uint8_t *) data)[index>>1] & 0xf0) >> 4;\r\n            }\r\n        }\r\n        else\r\n        {\r\n            val = baseNIndex;\r\n        }\r\n        val = isColorSpace() ? int2colorSpace[val] : int2base[val];\r\n        return val;\r\n    }\r\n    \/* ........... more codes omitted ................ *\/\r\n}\r\n<\/pre>\n
\u4f46\u5b9e\u9645\u4e0a\u8fd9\u4e9b\u7ec6\u8282\u5e76\u4e0d\u91cd\u8981\uff0c\u91cd\u8981\u662f\u5982\u4f55\u5305\u88c5\uff0c\u6211\u4eec\u7f16\u5199GenomeSequence_wrap.cpp\u6587\u4ef6\uff0c\u5305\u62ec\u5bf9\u4e0a\u8ff04\u4e2a\u51fd\u6570\u7684\u5c01\u88c5\uff0c\u6e90\u7801\u5982\u4e0b\uff1a<\/p>\n
\r\n#include "GenomeSequence.h"\r\n#include <string>\r\n\r\nextern "C"{\r\n    GenomeSequence* GenomeSequence_new(){ return new GenomeSequence();}\r\n    bool GenomeSequence_setReferenceName(GenomeSequence* gs, char* s) { \r\n        if (!gs) return false;\r\n        std::string str = s;\r\n        \/\/printf("Loading %s ...\\n", s);\r\n        if (!gs->setReferenceName(str)){\r\n            gs->open();\r\n        } else {\r\n            printf("Loading FAIL\\n");\r\n        }\r\n        return (gs->setReferenceName(str));\r\n    }\r\n    void GenomeSequence_close(GenomeSequence* gs) {if (gs) gs->close();};\r\n    int GenomeSequence_getNumBase(GenomeSequence* gs) {\r\n        if (!gs) {\r\n            printf("invalid gs\\n");\r\n            return -1;\r\n        }\r\n        return (gs->getNumberBases());\r\n    }\r\n    char GenomeSequence_getBase(GenomeSequence* gs, unsigned int i) { \r\n        if (gs) {\r\n            return (*gs)[i];\r\n        };\r\n    };\r\n}\r\n<\/pre>\n
\u7b2c\u4e8c\u6b65\u662f\u7f16\u8bd1\uff0c\u8bb0\u4f4f\u5355\u4e2aC\/C++\u6587\u4ef6\u7f16\u8bd1\u65f6\u4f7f\u7528-fPIC\u53c2\u6570\uff0c\u6700\u540e\u6253\u5305\u7684\u65f6\u5019\u7f16\u8bd1\u6210\u5171\u4eab\u5e93\uff0c\u6458\u5f55Makefile\u6587\u4ef6\u4e2d\u7247\u6bb5\u5982\u4e0b\uff1a<\/p>\n
\r\nlib:\r\n\tg++ -c -fPIC -I.\/lib GenomeSequence_wrap.c\r\n\tg++ -shared -Wl,-soname,libstatgen.so -o libstatgen.so  lib\/*.o lib\/samtools\/k*.o lib\/samtools\/bgzf.o *.o\r\n<\/pre>\n
\u6700\u540e\u4e00\u6b65\u662f\u5728Python\u4e2d\u5199\u4e00\u4e2a\u5c01\u88c5\u7c7b\uff0c\u6ce8\u610f\u524d\u4e24\u884c\u5f15\u5165ctypes\u5e93\uff0c\u4e4b\u540e\u5c31\u7528\u8fd9\u4e2a\u5e93\u8c03\u7528\u5305\u88c5\u51fd\u6570\u5c31\u884c\u3002
\n\u6ce8\u610f\uff1a\u6211\u5728GenomeSequence\u7c7b\u7684__getitem__\u4e2d\u4f7f\u7528\u4e86\u5982\u4f55\u6269\u5c55Python\u7684\u5bb9\u5668\u7c7b<\/a>\u4e00\u6587\u4e2d\u4ecb\u7ecd\u7684\u4e00\u4e9b\u6280\u5de7\uff0c\u8fd9\u6837\u53ef\u4ee5\u66f4\u7075\u6d3b\u7684\u4f7f\u7528\u4e0b\u6807\u6765\u8bbf\u95ee\u6570\u7ec4\u4e2d\u7684\u5143\u7d20\u3002<\/p>\n
\r\nfrom ctypes import cdll\r\nlib = cdll.LoadLibrary(".\/libstatgen.so")\r\n\r\nclass GenomeSequence:\r\n    def __init__ (self):\r\n        self.obj = lib.GenomeSequence_new()\r\n    def open(self, filename):\r\n        lib.GenomeSequence_setReferenceName(self.obj, filename)\r\n    def __len__ (self):\r\n        return lib.GenomeSequence_getNumBase(self.obj)\r\n    def __getitem__(self, key):\r\n        if isinstance(key, int):\r\n            return chr(lib.GenomeSequence_getBase(self.obj, key))\r\n        elif isinstance(key, slice):\r\n            return ''.join([self[x] for x in xrange(*key.indices(len(self)))])\r\n        elif isinstance(key, tuple):\r\n            return ''.join([self[i] for i in key])\r\n\r\n    def at(self, i):\r\n        return chr(lib.GenomeSequence_getBase(self.obj, i))\r\n    def close(self):\r\n        lib.GenomeSequence_close(self.obj)\r\n    \r\nif __name__ == '__main__':\r\n    gs = GenomeSequence ()\r\n    gs.open("\/home\/zhanxw\/statgen\/src\/karma\/test\/phiX.fa");\r\n    print len(gs)\r\n    seq = [(gs.at(i)) for i in xrange(60)]\r\n    print ''.join(seq)\r\n    print gs[0:10],gs[20:30]\r\n    print gs[0:10, 20:30]\r\n    print gs[-10:]\r\n    gs.close()\r\n    print "DONE"\r\n<\/pre>\n
\u672c\u6587\u4e3b\u8981\u53c2\u8003\u30101\u3011\u3002\u8fd9\u91cc\u7684\u65b9\u6cd5\u57fa\u672c\u91cd\u590d\u4e86\u30101\u3011\u4e2d\u7684\u6b65\u9aa4\u3002\u5199\u51fa\u672c\u6587\u4e2d\u7684\u4ee3\u7801\u5728\u4e8e\u8fdb\u4e00\u6b65\u9a8c\u8bc1ctypes\u5e93\u53ef\u4ee5\u7075\u6d3b\u7684\u5904\u7406C\/C++\u548cPython\u4e2d\u7684\u7b80\u5355\u6570\u636e\u7c7b\u578bint, char*\u3002<\/p>\n
\u30101\u3011Calling C\/C++ from python?<\/a><\/p>\n","protected":false},"excerpt":{"rendered":"
\u5982\u4f55\u5728Python\u4e2d\u8c03\u7528C\/C++\u4ee3\u7801 How to mix C\/C++ code in Python \u672c\u6587\u4ecb\u7ecd\u4e00\u79cd\u624b\u52a8\u7684\u3001\u7b80\u5355\u7684\u5728Python\u4e2d\u4f7f\u7528C\/C++\u4ee3\u7801\u7684\u65b9\u5f0f\u3002\u8fd9\u4e2a\u65b9\u6cd5\u4e3b\u8981\u4f7f\u7528\u4e86ctypes\u6a21\u5757\u3002\u5176\u4ed6\u7684\u6df7\u5408Python\uff0cC\/C++\u7f16\u7a0b\u7684\u65b9\u6cd5\u8fd8\u6709Swig \u548c Boost.Python\u3002\u524d\u4e00\u79cd\u65b9\u6cd5\u9700\u8981\u5199\u4e00\u4e2a\u63a5\u53e3\u6587\u4ef6\uff08interface\uff09\uff0c\u800c\u540e\u4e00\u79cd\u9700\u8981\u4f7f\u7528\u5e9e\u5927\u3001\u6df1\u5965\u7684boost\u7c7b\u5e93\uff0c\u540e\u4e24\u8005\u9002\u5408\u53ef\u80fd\u9002\u5408\u66f4\u590d\u6742\u7684\u60c5\u51b5\uff0c\u8fd9\u91cc\u53ea\u4ecb\u7ecd\u7b2c\u4e00\u79cd\u65b9\u6cd5\u3002 \u6df7\u5408C\/C++\u4ee3\u7801\u9700\u8981\u8fd9\u51e0\u6b65\uff1a 1. \u5305\u88c5\u63a5\u53e3 C\/C++ wrap functions up 2. \u6253\u5305\u6210\u5171\u4eab\u5e93 Compiling C\/C++ code and pack it to shared library 3. Python\u4e2d\u5bfc\u5165\u5171\u4eab\u5e93 Python imports shared library \u5148\u4ecb\u7ecd\u4e00\u4e0b\u5317\u4eac\uff0c\u8fd9\u91cc\u6211\u7684C++\u7c7bGenomeSequence\u4f7f\u7528\u4e86\u6a21\u677f\uff08Template\uff09\u548cMemorymap\uff0c\u8fd9\u662f\u4e00\u4e2a\u8bbf\u95ee\u57fa\u56e0\u5e8f\u5217\u7684\u7c7b\uff0c\u6bd4\u5982\u5982\u679c\u4e00\u4e2a\u751f\u7269\u5e8f\u5217\u662fGAGTTTTATCGCTTCCATGACGCAGAAGTTAACACT… \u6211\u4eec\u7684\u7c7b\u662fgs\uff0c\u90a3\u4e48gs[0] = ‘G’, gs[1]=’A’ …. \u6458\u5f55\u76f8\u5173\u7684\u51fd\u6570\u5982\u4e0b\uff1a class GenomeSequence : public genomeSequenceArray { public: \/\/\/ Simple constructor – no implicit […]<\/p>\n","protected":false},"author":2,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[4],"tags":[56,55,53],"class_list":["post-206","post","type-post","status-publish","format-standard","hentry","category-code","tag-bind","tag-c","tag-python"],"_links":{"self":[{"href":"https:\/\/zhanxw.com\/blog\/wp-json\/wp\/v2\/posts\/206","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/zhanxw.com\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/zhanxw.com\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/zhanxw.com\/blog\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/zhanxw.com\/blog\/wp-json\/wp\/v2\/comments?post=206"}],"version-history":[{"count":0,"href":"https:\/\/zhanxw.com\/blog\/wp-json\/wp\/v2\/posts\/206\/revisions"}],"wp:attachment":[{"href":"https:\/\/zhanxw.com\/blog\/wp-json\/wp\/v2\/media?parent=206"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/zhanxw.com\/blog\/wp-json\/wp\/v2\/categories?post=206"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/zhanxw.com\/blog\/wp-json\/wp\/v2\/tags?post=206"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}