{"id":72700,"date":"2026-11-15T09:54:15","date_gmt":"2026-11-15T01:54:15","guid":{"rendered":"https:\/\/www.biocloudservice.com\/wordpress\/?p=72700"},"modified":"2026-11-15T09:54:15","modified_gmt":"2026-11-15T01:54:15","slug":"gtdbtk-msa-mask-linewrap-effective-residues","status":"publish","type":"post","link":"https:\/\/www.biocloudservice.com\/wordpress\/gtdbtk-msa-mask-linewrap-effective-residues\/","title":{"rendered":"GTDB-Tk \u7684\u6bd4\u5bf9\u77e9\u9635\u600e\u6837\u68c0\u67e5\uff1f\u5b9e\u8dd1\u516d\u79cd\u63a9\u7801\uff0c\u627e\u51fa\u6b63\u5e38\u7ed3\u675f\u5374\u5c11\u4e86\u4e00\u534a\u5217\u7684\u539f\u56e0"},"content":{"rendered":"
\n

\u62ff\u5230\u4e00\u4efd\u5fae\u751f\u7269\u57fa\u56e0\u7ec4\u5206\u7c7b\u7ed3\u679c\u4ee5\u540e\uff0c\u5f88\u591a\u5206\u6790\u4f1a\u76f4\u63a5\u63d0\u53d6\u7269\u79cd\u540d\u79f0\uff0c\u518d\u5408\u5e76\u5230\u4e30\u5ea6\u8868\u3002\u771f\u6b63\u9700\u8981\u8ffd\u95ee\u7684\u8fd8\u6709\u53c2\u8003\u7248\u672c\u3001\u5206\u7c7b\u4f9d\u636e\u548c\u53c2\u4e0e\u6bd4\u8f83\u7684\u6709\u6548\u4f4d\u70b9\u3002\u5c24\u5176\u5728\u6574\u7406\u6807\u8bb0\u86cb\u767d\u6bd4\u5bf9\u3001\u8ffd\u52a0\u6837\u672c\u6216\u6784\u5efa\u81ea\u5b9a\u4e49\u7cfb\u7edf\u6811\u65f6\uff0c\u4e00\u5904\u63a9\u7801\u683c\u5f0f\u53d8\u5316\uff0c\u5c31\u53ef\u80fd\u6539\u53d8\u6bcf\u4e2a\u6837\u672c\u4fdd\u7559\u4e0b\u6765\u7684\u5e8f\u5217\u4fe1\u606f\u3002<\/p>\n

\u672c\u6587\u5b89\u88c5 GTDB-Tk 2.8.0\uff0c\u5b9e\u9645\u8c03\u7528\u8be5\u7248\u672c\u7684\u539f\u7248\u6bd4\u5bf9\u88c1\u5217\u65b9\u6cd5\uff0c\u6bd4\u8f83\u516d\u79cd\u63a9\u7801\u8f93\u5165\u3002\u5b9e\u9a8c\u91c7\u7528\u81ea\u5efa\u7684\u56db\u6761\u77ed\u86cb\u767d\u6bd4\u5bf9\uff0c\u8fd0\u884c\u8303\u56f4\u8986\u76d6\u77e9\u9635\u88c1\u5217\u4e0e\u8f93\u51fa\u6838\u5bf9\u3002\u6211\u4eec\u540c\u65f6\u7ed3\u5408\u5b98\u65b9\u5206\u7c7b\u6587\u6863\uff0c\u8bf4\u660e\u8fd9\u4e9b\u68c0\u67e5\u5e94\u5f53\u653e\u5728\u5b9e\u9645\u5206\u6790\u7684\u4ec0\u4e48\u4f4d\u7f6e\uff0c\u4ee5\u53ca\u5206\u7c7b\u8868\u91cc\u54ea\u4e9b\u5b57\u6bb5\u503c\u5f97\u4e00\u8d77\u4fdd\u5b58\u3002<\/p>\n

\"\u63a9\u7801\u6298\u884c\u540e\u5c11\u4e86\u5341\u5217\u3002GTDB-Tk
GTDB-Tk 2.8.0 \u539f\u7248\u88c1\u5217\u65b9\u6cd5\u5b9e\u8dd1<\/figcaption><\/figure>\n

\u5148\u786e\u5b9a\u81ea\u5df1\u5728\u68c0\u67e5\u54ea\u4e00\u6bb5\u5206\u6790<\/h2>\n

GTDB-Tk \u5c06\u57fa\u56e0\u7ec4\u4e0e\u53c2\u8003\u5206\u7c7b\u4f53\u7cfb\u8054\u7cfb\u8d77\u6765\u3002\u5f53\u524d\u5206\u7c7b\u6d41\u7a0b\u4f1a\u5148\u8fdb\u884c\u6838\u82f7\u9178\u76f8\u4f3c\u6027\u7b5b\u67e5\uff0c\u6ee1\u8db3\u76f8\u5e94\u6761\u4ef6\u7684\u57fa\u56e0\u7ec4\u53ef\u4ee5\u5f97\u5230\u7269\u79cd\u5f52\u5c5e\uff0c\u5176\u4f59\u57fa\u56e0\u7ec4\u7ee7\u7eed\u8fdb\u5165\u6807\u8bb0\u8bc6\u522b\u3001\u86cb\u767d\u6bd4\u5bf9\u548c\u53c2\u8003\u6811\u653e\u7f6e\u7b49\u73af\u8282\u3002\u6d41\u7a0b\u4f1a\u6839\u636e\u8bc1\u636e\u8def\u5f84\u5199\u5165\u4e0d\u540c\u7684\u5206\u7c7b\u65b9\u6cd5\uff0c\u56e0\u6b64\u8bfb\u53d6\u7ed3\u679c\u65f6\u9700\u8981\u4fdd\u7559\u65b9\u6cd5\u5217\u548c\u76f8\u5173\u53c2\u8003\u4fe1\u606f\u3002\u5b98\u65b9\u5206\u7c7b\u6d41\u7a0b<\/a><\/p>\n

\u5982\u679c\u4e00\u4e2a\u57fa\u56e0\u7ec4\u5df2\u7ecf\u901a\u8fc7\u76f8\u4f3c\u6027\u7b5b\u67e5\u83b7\u5f97\u5206\u7c7b\uff0c\u540e\u9762\u6ca1\u6709\u5bf9\u5e94\u7684\u6811\u653e\u7f6e\u8bb0\u5f55\uff0c\u53ef\u4ee5\u5148\u68c0\u67e5\u5206\u7c7b\u65b9\u6cd5\u53ca\u662f\u5426\u542f\u7528\u4e86\u989d\u5916\u653e\u7f6e\u9009\u9879\u3002\u53cd\u8fc7\u6765\uff0c\u4e00\u4e2a\u8fdb\u5165\u6807\u8bb0\u6bd4\u5bf9\u7684\u57fa\u56e0\u7ec4\uff0c\u5373\u4f7f\u5e8f\u5217\u6587\u4ef6\u751f\u6210\u6210\u529f\uff0c\u4e5f\u9700\u8981\u68c0\u67e5\u6709\u6548\u6c28\u57fa\u9178\u6bd4\u4f8b\u3002\u628a\u201c\u6587\u4ef6\u5b58\u5728\u201d\u201c\u77e9\u9635\u6709\u5217\u201d\u201c\u6837\u672c\u6709\u8db3\u591f\u53ef\u6bd4\u8f83\u6b8b\u57fa\u201d\u5206\u6210\u4e09\u9879\u68c0\u67e5\uff0c\u80fd\u591f\u66f4\u5feb\u5224\u65ad\u95ee\u9898\u53d1\u751f\u5728\u6570\u636e\u51c6\u5907\u8fd8\u662f\u5206\u7c7b\u8bc1\u636e\u9636\u6bb5\u3002<\/p>\n

\u672c\u6587\u4e13\u95e8\u68c0\u67e5\u7b2c\u4e8c\u6761\u8def\u5f84\u4e2d\u7684\u77e9\u9635\u5904\u7406\u3002GTDB-Tk \u63d0\u4f9b\u63a9\u7801\u88c1\u5217\u529f\u80fd\uff0c\u53ef\u4ee5\u4f7f\u7528\u53c2\u8003\u5305\u7684\u63a9\u7801\uff0c\u4e5f\u53ef\u4ee5\u6307\u5b9a\u81ea\u5df1\u7684\u63a9\u7801\u6587\u4ef6\u3002\u5b98\u65b9\u793a\u4f8b\u4e2d\u7684\u6bcf\u4e2a\u96f6\u6216\u4e00\uff0c\u5bf9\u5e94\u539f\u59cb\u6bd4\u5bf9\u7684\u4e00\u5217\uff0c\u4e00\u4ee3\u8868\u4fdd\u7559\u3002\u63a9\u7801\u7d22\u5f15\u9488\u5bf9\u5bf9\u9f50\u540e\u7684\u5750\u6807\uff0c\u7f3a\u53e3\u540c\u6837\u5360\u636e\u4e00\u4e2a\u4f4d\u7f6e\u3002\u5b98\u65b9\u88c1\u5217\u547d\u4ee4<\/a><\/p>\n

\u7528\u56db\u6761\u77ed\u5e8f\u5217\u8ba9\u53d8\u5316\u770b\u5f97\u89c1<\/h2>\n

\u6211\u4eec\u6784\u9020\u4e00\u4e2a\u56db\u884c\u56db\u5341\u5217\u7684\u86cb\u767d\u6bd4\u5bf9\u3002\u7b2c\u4e00\u884c\u5168\u90e8\u662f\u660e\u786e\u7684\u6c28\u57fa\u9178\uff0c\u7b2c\u4e8c\u884c\u53ea\u6709\u5de6\u534a\u6bb5\u5b58\u5728\u6b8b\u57fa\uff0c\u7b2c\u4e09\u884c\u53ea\u6709\u53f3\u534a\u6bb5\u5b58\u5728\u6b8b\u57fa\uff0c\u7b2c\u56db\u884c\u5de6\u534a\u6bb5\u5168\u90e8\u4e3a\u672a\u77e5\u6c28\u57fa\u9178\u7b26\u53f7\u3002\u5b83\u4eec\u7684\u884c\u957f\u5ea6\u76f8\u540c\uff0c\u4fe1\u606f\u5206\u5e03\u660e\u663e\u4e0d\u540c\uff0c\u9002\u5408\u89c2\u5bdf\u63a9\u7801\u4f4d\u7f6e\u548c\u7f3a\u5931\u503c\u7684\u5f71\u54cd\u3002<\/p>\n

\u4e3a\u65b9\u4fbf\u624b\u5de5\u6838\u5bf9\uff0c\u6bcf\u4e8c\u5341\u5217\u91c7\u7528\u4e8c\u5341\u79cd\u5e38\u89c1\u6c28\u57fa\u9178\u6309\u56fa\u5b9a\u6b21\u5e8f\u6392\u5217\u3002\u8fd9\u4e2a\u77e9\u9635\u53ea\u7528\u4e8e\u9a8c\u8bc1\u7a0b\u5e8f\u5bf9\u6587\u4ef6\u5185\u5bb9\u7684\u5904\u7406\u89c4\u5219\u3002\u8bfb\u8005\u53ef\u4ee5\u9010\u5b57\u6570\u51fa\u7559\u4e0b\u7684\u4f4d\u70b9\uff0c\u4e5f\u53ef\u4ee5\u628a\u5b9e\u9a8c\u811a\u672c\u4e2d\u7684\u77e9\u9635\u66ff\u6362\u6210\u81ea\u5df1\u7684\u6807\u8bb0\u6bd4\u5bf9\uff0c\u7ee7\u7eed\u6267\u884c\u76f8\u540c\u7684\u683c\u5f0f\u68c0\u67e5\u3002<\/p>\n

>complete\r\nACDEFGHIKLMNPQRSTVWYACDEFGHIKLMNPQRSTVWY\r\n>left_only\r\nACDEFGHIKLMNPQRSTVWY--------------------\r\n>right_only\r\n--------------------ACDEFGHIKLMNPQRSTVWY\r\n>unknown_left\r\nXXXXXXXXXXXXXXXXXXXXACDEFGHIKLMNPQRSTVWY\r\n<\/code><\/pre>\n
\u672c\u6b21\u73af\u5883\u4f7f\u7528 Python 3.12\u3001GTDB-Tk 2.8.0\u3001NumPy 1.26.4 \u548c DendroPy 4.6.4\u3002\u811a\u672c\u8c03\u7528\u5b89\u88c5\u5305\u4e2d\u7684\u539f\u7248\u65b9\u6cd5\uff0c\u5b8c\u6574\u4fdd\u5b58\u8f93\u5165\u3001\u63a9\u7801\u3001\u8f93\u51fa\u4ee5\u53ca\u5f02\u5e38\u8bb0\u5f55\u3002\u8fd9\u4e2a\u65b9\u6cd5\u4e5f\u662f\u88c1\u5217\u529f\u80fd\u5b9e\u9645\u4f7f\u7528\u7684\u5b9e\u73b0\uff0c\u4fbf\u4e8e\u5728\u56fa\u5b9a\u7684\u5fae\u578b\u8f93\u5165\u4e0a\u89c2\u5bdf\u884c\u4e3a\uff0c\u5b8c\u6574\u57fa\u56e0\u7ec4\u5206\u7c7b\u53e6\u5916\u9700\u8981\u5339\u914d\u7684\u53c2\u8003\u6570\u636e\u53ca\u76f8\u5173\u8fd0\u884c\u4f9d\u8d56\u3002\u672c\u6b21\u7248\u672c\u6e90\u7801<\/a><\/p>\n
from gtdbtk.misc import Misc\r\n\r\nMisc().trim_msa(\r\n    "aligned.faa",\r\n    "file",\r\n    "balanced.mask",\r\n    "balanced.faa",\r\n)\r\n<\/code><\/pre>\n
\u76f8\u540c\u7684\u5217\u6570\uff0c\u4e5f\u53ef\u80fd\u4fdd\u7559\u5b8c\u5168\u4e0d\u540c\u7684\u8bc1\u636e<\/h2>\n
\u7b2c\u4e00\u4efd\u63a9\u7801\u91c7\u7528\u4e00\u96f6\u4ea4\u66ff\uff0c\u5171\u4fdd\u7559\u4e8c\u5341\u5217\u3002\u5b8c\u6574\u5e8f\u5217\u7559\u4e0b\u4e8c\u5341\u4e2a\u660e\u786e\u6b8b\u57fa\uff0c\u5de6\u4fa7\u6709\u5e8f\u5217\u548c\u53f3\u4fa7\u6709\u5e8f\u5217\u7684\u4e24\u4e2a\u6837\u672c\u5404\u7559\u4e0b\u5341\u4e2a\u660e\u786e\u6b8b\u57fa\uff0c\u672a\u77e5\u7b26\u53f7\u6837\u672c\u4e5f\u53ea\u6709\u5341\u4e2a\u660e\u786e\u6b8b\u57fa\u3002<\/p>\n
\u7b2c\u4e8c\u4efd\u63a9\u7801\u53ea\u4fdd\u7559\u5de6\u534a\u6bb5\uff0c\u4e5f\u5f97\u5230\u4e8c\u5341\u5217\u3002\u5de6\u4fa7\u6837\u672c\u7684\u660e\u786e\u6b8b\u57fa\u5360\u6bd4\u5347\u5230\u767e\u5206\u4e4b\u767e\uff0c\u53f3\u4fa7\u6837\u672c\u964d\u5230\u96f6\uff0c\u672a\u77e5\u7b26\u53f7\u6837\u672c\u4e5f\u964d\u5230\u96f6\u3002\u4e24\u4efd\u8f93\u51fa\u7684\u6587\u4ef6\u7ed3\u6784\u90fd\u6b63\u5e38\uff0c\u6bcf\u884c\u957f\u5ea6\u90fd\u76f8\u540c\uff0c\u5b8c\u6574\u6837\u672c\u4e5f\u90fd\u4fdd\u7559\u4e8c\u5341\u4e2a\u6b8b\u57fa\uff0c\u4f46\u5b83\u4eec\u5bf9\u5176\u4ed6\u6837\u672c\u63d0\u4f9b\u7684\u6bd4\u8f83\u6761\u4ef6\u5df2\u7ecf\u53d1\u751f\u53d8\u5316\u3002<\/p>\n
\n\n\n\n\n\n\n\n\n
\u63a9\u7801\u65b9\u5f0f<\/th>\n\u8f93\u51fa\u5217\u6570<\/th>\n\u5de6\u4fa7\u6837\u672c\u660e\u786e\u6b8b\u57fa\u6bd4\u4f8b<\/th>\n\u53f3\u4fa7\u6837\u672c\u660e\u786e\u6b8b\u57fa\u6bd4\u4f8b<\/th>\n\u672a\u77e5\u7b26\u53f7\u6837\u672c\u660e\u786e\u6b8b\u57fa\u6bd4\u4f8b<\/th>\n<\/tr>\n<\/thead>\n
\u5168\u957f\u4e00\u96f6\u4ea4\u66ff<\/td>\n20<\/td>\n50%<\/td>\n50%<\/td>\n50%<\/td>\n<\/tr>\n
\u4ec5\u4fdd\u7559\u5de6\u534a\u6bb5<\/td>\n20<\/td>\n100%<\/td>\n0%<\/td>\n0%<\/td>\n<\/tr>\n
\u4ea4\u66ff\u63a9\u7801\u6298\u6210\u4e24\u884c<\/td>\n10<\/td>\n100%<\/td>\n0%<\/td>\n0%<\/td>\n<\/tr>\n
\u53ea\u6709\u524d\u4e8c\u5341\u4f4d\u7684\u77ed\u63a9\u7801<\/td>\n10<\/td>\n100%<\/td>\n0%<\/td>\n0%<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n
\u8fd9\u91cc\u7684\u6bd4\u4f8b\u7531\u5b9e\u9a8c\u811a\u672c\u6309\u4e8c\u5341\u79cd\u660e\u786e\u6c28\u57fa\u9178\u91cd\u65b0\u8ba1\u7b97\uff0c\u5206\u6bcd\u662f\u88c1\u5217\u540e\u7684\u5217\u6570\u3002\u5b83\u9002\u5408\u6838\u5bf9\u672c\u5b9e\u9a8c\u7684\u6709\u6548\u4fe1\u606f\u91cf\u3002\u5b9e\u9645\u5206\u7c7b\u8868\u4e2d\u7684\u5b57\u6bb5\u6709\u81ea\u5df1\u7684\u7a0b\u5e8f\u5b9a\u4e49\uff0c\u5f15\u7528\u65f6\u5e94\u6838\u5bf9\u76f8\u5e94\u7248\u672c\u7684\u8ba1\u7b97\u65b9\u5f0f\uff0c\u907f\u514d\u628a\u4e24\u79cd\u7edf\u8ba1\u53e3\u5f84\u6df7\u5199\u3002<\/p>\n
\u8fd9\u4e00\u7ec4\u5bf9\u7167\u63d0\u793a\u6211\u4eec\uff0c\u5728\u8c03\u6574\u63a9\u7801\u65f6\uff0c\u5355\u770b\u77e9\u9635\u603b\u957f\u5ea6\u5f88\u5bb9\u6613\u9057\u6f0f\u6837\u672c\u5c42\u9762\u7684\u53d8\u5316\u3002\u53ef\u4ee5\u540c\u65f6\u8f93\u51fa\u6bcf\u884c\u660e\u786e\u6b8b\u57fa\u6570\u3001\u7f3a\u53e3\u6570\u3001\u672a\u77e5\u7b26\u53f7\u6570\u53ca\u4fdd\u7559\u6bd4\u4f8b\u3002\u5bf9\u4e8e\u67d0\u4e00\u6279\u6837\u672c\u96c6\u4e2d\u4e22\u5931\u7279\u5b9a\u6807\u8bb0\u7684\u60c5\u51b5\uff0c\u6574\u4f53\u5e73\u5747\u5360\u6bd4\u8fd8\u53ef\u80fd\u63a9\u76d6\u7ec4\u95f4\u5dee\u5f02\uff0c\u56e0\u6b64\u9700\u8981\u6309\u7814\u7a76\u5206\u7ec4\u68c0\u67e5\u5206\u5e03\u3002<\/p>\n
\u4e3a\u4ec0\u4e48\u628a\u63a9\u7801\u6298\u6210\u4e24\u884c\u4f1a\u6539\u53d8\u8f93\u51fa<\/h2>\n
\u7b2c\u4e09\u6b21\u8fd0\u884c\u53ea\u6539\u53d8\u63a9\u7801\u7684\u6587\u4ef6\u6392\u7248\u3002\u539f\u672c\u56db\u5341\u4e2a\u5b57\u7b26\u5199\u5728\u4e00\u884c\uff0c\u6211\u4eec\u5c06\u5b83\u4eec\u6298\u6210\u4e24\u884c\uff0c\u6bcf\u884c\u4e8c\u5341\u4e2a\u5b57\u7b26\u3002\u8fd0\u884c\u6b63\u5e38\u7ed3\u675f\uff0c\u8f93\u51fa\u5374\u53ea\u5269\u5341\u5217\uff0c\u5185\u5bb9\u4e0e\u53ea\u63d0\u4f9b\u524d\u4e8c\u5341\u4f4d\u63a9\u7801\u7684\u7b2c\u56db\u6b21\u8fd0\u884c\u5b8c\u5168\u76f8\u540c\u3002<\/p>\n
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\u7ed9\u88c1\u5217\u8fc7\u7a0b\u8865\u4e0a\u53ef\u6267\u884c\u7684\u68c0\u67e5<\/h2>\n
\u5f00\u59cb\u88c1\u5217\u524d\uff0c\u5148\u8981\u6c42\u8f93\u5165\u6bd4\u5bf9\u4e2d\u7684\u6240\u6709\u5e8f\u5217\u7b49\u957f\uff0c\u5e8f\u5217\u6807\u8bc6\u552f\u4e00\uff0c\u63a9\u7801\u53ea\u5305\u542b\u96f6\u548c\u4e00\uff0c\u63a9\u7801\u957f\u5ea6\u4e0e\u6bd4\u5bf9\u5217\u6570\u5b8c\u5168\u76f8\u7b49\u3002\u4e0b\u9762\u7684\u4ee3\u7801\u9002\u7528\u4e8e\u660e\u786e\u8981\u6c42\u5355\u884c\u63a9\u7801\u7684\u8fd9\u4efd\u5b9e\u9a8c\uff0c\u4e5f\u4f1a\u628a\u8bef\u6298\u884c\u7684\u6587\u4ef6\u76f4\u63a5\u62e6\u4e0b\u6765\u3002<\/p>\n
from pathlib import Path\r\nfrom gtdbtk.biolib_lite.seq_io import read_fasta\r\n\r\nrows = read_fasta("aligned.faa", False)\r\nlengths = {len(seq) for seq in rows.values()}\r\nassert rows and len(lengths) == 1\r\ncolumns = lengths.pop()\r\n\r\nmask_lines = Path("balanced.mask").read_text().splitlines()\r\nassert len(mask_lines) == 1\r\nmask = mask_lines[0]\r\nassert set(mask) <= {"0", "1"}\r\nassert len(mask) == columns\r\nassert mask.count("1") > 0\r\n<\/code><\/pre>\n
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