基因 ID 匹配利器

阅读原文时间：2023年08月15日阅读：2

一、背景

对于每个生物信息分析的人来说，ID 匹配（映射）是一项非常常见，但又很繁琐的任务。假设，我们有一个来自上游分析的 gene symbol 或报告的 ID 列表，然后我们的下一个分析却需要使用基因 ID（例如 Entrez gene id 或 Ensembl gene id）。这时候，我们就希望将基因符号或报告的 ID 的列表转换为相应的基因 ID。

在开始介绍今天的主角 mygene 前，我们先来认识一下 MyGene.info。

MyGene.info 是一个由 NIH(美国国立卫生研究院)/NIGMS 资助，用于提供简单易用的 REST Web 服务来查询/检索基因注释数据的 API。 MyGene.info 目前包含了 NCBI Entrez、Ensembl、Uniprot、UCSC 在内的 20 多个数据库，MyGene.info 会每周从这些数据库中进行数据更新。虽然 MyGene.info 中包含的各个数据源可能有数据使用限制，但 MyGene.info 本身的服务是免费的，其源码托管在：https://github.com/biothings/mygene.info。

MyGene.info 提供两种简单的 Web 服务：一种用于基因查询，另一种用于基因注释检索。两者都以 JSON 格式返回结果。截至 2019 年 3 月 6 日，MyGene.info 最新的 API 为 v3，相比 v1、v2，v3 新增了以下几点内容：

Refseq accession number now contains version
"ensembl", "refseq" and "accession" contains associations between RNA and protein
Better mapping between Ensembl and Entrez gene IDs
JSON structure slightly changed
and more bugfixes

虽然 MyGene.info 是一个在线的 web 服务，但它同时也提供了基于 R 和 Python 的第三方模块，源码均在 GitHub 上开源：

MyGene R Client：https://github.com/biothings/mygene.R
MyGene Python Client：https://github.com/biothings/mygene.py

在这里，我们简单展示如何在 Python 中使用 mygene 模块来快速轻松地进行类似的 ID 匹配（映射）。mygene 本质上是一个方便的 Python 模块，通过这个模块我们可以访问 MyGene.info 的基因查询 Web 服务。

二、mygene 安装与使用

在 Python 中 mygene 的安装非常简单，直接使用 pip 就可以安装。

pip&nbsp;install&nbsp;mygene

mygene 安装完成后，现在我们只需要导入它并实例化 mygeneinfo 类：

import&nbsp;mygenemg&nbsp;=&nbsp;mygene.MyGeneInfo()

假设 xli 是我们要转换为 entrez gene id 的 gene symbol 列表：

xli&nbsp;=&nbsp;['CCDC83',&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;'MAST3',&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;'FLOT1',&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;'RPL11',&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;'ZDHHC20',&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;'LUC7L3',&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;'SNORD49A',&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;'CTSH',&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;'ACOT8']

然后我们调用 querymany 方法，并告诉它我们输入的是 "符号(symbol)"，我们想要返回的是 "entrezgene"(Entrez gene ids)：

>>>&nbsp;out&nbsp;=&nbsp;mg.querymany(xli,&nbsp;scopes='symbol',&nbsp;fields='entrezgene',&nbsp;species='human')querying&nbsp;1-9...done.Finished.>>>&nbsp;for&nbsp;i&nbsp;in&nbsp;out:...&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;print(i)...{u'entrezgene':&nbsp;u'220047',&nbsp;u'query':&nbsp;u'CCDC83',&nbsp;u'_id':&nbsp;u'220047',&nbsp;u'_score':&nbsp;87.6894}{u'entrezgene':&nbsp;u'23031',&nbsp;u'query':&nbsp;u'MAST3',&nbsp;u'_id':&nbsp;u'23031',&nbsp;u'_score':&nbsp;88.66032}{u'entrezgene':&nbsp;u'10211',&nbsp;u'query':&nbsp;u'FLOT1',&nbsp;u'_id':&nbsp;u'10211',&nbsp;u'_score':&nbsp;89.97141}{u'entrezgene':&nbsp;u'6135',&nbsp;u'query':&nbsp;u'RPL11',&nbsp;u'_id':&nbsp;u'6135',&nbsp;u'_score':&nbsp;82.54278}{u'entrezgene':&nbsp;u'253832',&nbsp;u'query':&nbsp;u'ZDHHC20',&nbsp;u'_id':&nbsp;u'253832',&nbsp;u'_score':&nbsp;87.46338}{u'entrezgene':&nbsp;u'51747',&nbsp;u'query':&nbsp;u'LUC7L3',&nbsp;u'_id':&nbsp;u'51747',&nbsp;u'_score':&nbsp;86.709984}{u'entrezgene':&nbsp;u'26800',&nbsp;u'query':&nbsp;u'SNORD49A',&nbsp;u'_id':&nbsp;u'26800',&nbsp;u'_score':&nbsp;107.5259}{u'entrezgene':&nbsp;u'1512',&nbsp;u'query':&nbsp;u'CTSH',&nbsp;u'_id':&nbsp;u'1512',&nbsp;u'_score':&nbsp;85.86504}{u'entrezgene':&nbsp;u'10005',&nbsp;u'query':&nbsp;u'ACOT8',&nbsp;u'_id':&nbsp;u'10005',&nbsp;u'_score':&nbsp;84.415535}

上面程序的匹配（映射）结果作为字典列表返回。每个字典都包含我们要求返回的字段，在本例中为 "entrezgene" 字段。每个字典还返回匹配的查询词 "query" 和内部 id("_id")，大部分时间与 "entrezgene" 相同（如果基因仅来自 Ensembl，则为 ensembl 基因 id）。

如果我们只需要返回 Ensembl gene ids 时，只需要把 fields 参数值改成 'ensembl.gene' 即可：

>>>&nbsp;out&nbsp;=&nbsp;mg.querymany(xli,&nbsp;scopes='symbol',&nbsp;fields='ensembl.gene',&nbsp;species='human')querying&nbsp;1-9...done.Finished.>>>&nbsp;for&nbsp;i&nbsp;in&nbsp;out:...&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;print&nbsp;i...{u'ensembl':&nbsp;{u'gene':&nbsp;u'ENSG00000150676'},&nbsp;u'query':&nbsp;u'CCDC83',&nbsp;u'_id':&nbsp;u'220047',&nbsp;u'_score':&nbsp;87.86632}{u'ensembl':&nbsp;{u'gene':&nbsp;u'ENSG00000099308'},&nbsp;u'query':&nbsp;u'MAST3',&nbsp;u'_id':&nbsp;u'23031',&nbsp;u'_score':&nbsp;88.42681}{u'ensembl':&nbsp;[{u'gene':&nbsp;u'ENSG00000230143'},&nbsp;{u'gene':&nbsp;u'ENSG00000236271'},&nbsp;{u'gene':&nbsp;u'ENSG00000137312'},&nbsp;{u'gene':&nbsp;u'ENSG00000206379'},&nbsp;{u'gene':&nbsp;u'ENSG00000232280'},&nbsp;{u'gene':&nbsp;u'ENSG00000206480'},&nbsp;{u'gene':&nbsp;u'ENSG00000224740'},&nbsp;{u'gene':&nbsp;u'ENSG00000223654'}],&nbsp;u'query':&nbsp;u'FLOT1',&nbsp;u'_id':&nbsp;u'10211',&nbsp;u'_score':&nbsp;90.23538}{u'ensembl':&nbsp;{u'gene':&nbsp;u'ENSG00000142676'},&nbsp;u'query':&nbsp;u'RPL11',&nbsp;u'_id':&nbsp;u'6135',&nbsp;u'_score':&nbsp;82.40764}{u'ensembl':&nbsp;{u'gene':&nbsp;u'ENSG00000180776'},&nbsp;u'query':&nbsp;u'ZDHHC20',&nbsp;u'_id':&nbsp;u'253832',&nbsp;u'_score':&nbsp;87.6894}{u'ensembl':&nbsp;{u'gene':&nbsp;u'ENSG00000108848'},&nbsp;u'query':&nbsp;u'LUC7L3',&nbsp;u'_id':&nbsp;u'51747',&nbsp;u'_score':&nbsp;86.635506}{u'ensembl':&nbsp;{u'gene':&nbsp;u'ENSG00000277370'},&nbsp;u'query':&nbsp;u'SNORD49A',&nbsp;u'_id':&nbsp;u'26800',&nbsp;u'_score':&nbsp;107.55141}{u'ensembl':&nbsp;{u'gene':&nbsp;u'ENSG00000103811'},&nbsp;u'query':&nbsp;u'CTSH',&nbsp;u'_id':&nbsp;u'1512',&nbsp;u'_score':&nbsp;85.88113}{u'ensembl':&nbsp;{u'gene':&nbsp;u'ENSG00000101473'},&nbsp;u'query':&nbsp;u'ACOT8',&nbsp;u'_id':&nbsp;u'10005',&nbsp;u'_score':&nbsp;83.99602}

如果输入 id 没有匹配的基因，mygene 将在屏幕输出中打印相关的通知。此查询条目返回的字典中将包含 "notfound" 值为 True 的关键字。

>>>&nbsp;xli&nbsp;=&nbsp;['CCDC83',&nbsp;'MAST3',&nbsp;'FLOT1',&nbsp;'RPL11',&nbsp;'Gm10494']>>>&nbsp;out&nbsp;=&nbsp;mg.querymany(xli,&nbsp;scopes='symbol',&nbsp;fields='entrezgene',&nbsp;species='human')querying&nbsp;1-5...done.Finished.1&nbsp;input&nbsp;query&nbsp;terms&nbsp;found&nbsp;no&nbsp;hit:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;[u'Gm10494']Pass&nbsp;"returnall=True"&nbsp;to&nbsp;return&nbsp;complete&nbsp;lists&nbsp;of&nbsp;duplicate&nbsp;or&nbsp;missing&nbsp;query&nbsp;terms.>>>&nbsp;for&nbsp;i&nbsp;in&nbsp;out:...&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;print(i)...{u'entrezgene':&nbsp;u'220047',&nbsp;u'query':&nbsp;u'CCDC83',&nbsp;u'_id':&nbsp;u'220047',&nbsp;u'_score':&nbsp;87.6894}{u'entrezgene':&nbsp;u'23031',&nbsp;u'query':&nbsp;u'MAST3',&nbsp;u'_id':&nbsp;u'23031',&nbsp;u'_score':&nbsp;88.89522}{u'entrezgene':&nbsp;u'10211',&nbsp;u'query':&nbsp;u'FLOT1',&nbsp;u'_id':&nbsp;u'10211',&nbsp;u'_score':&nbsp;89.862946}{u'entrezgene':&nbsp;u'6135',&nbsp;u'query':&nbsp;u'RPL11',&nbsp;u'_id':&nbsp;u'6135',&nbsp;u'_score':&nbsp;82.584694}{u'query':&nbsp;u'Gm10494',&nbsp;u'notfound':&nbsp;True}

xli&nbsp;=&nbsp;['DDX26B',&nbsp;'CCDC83',&nbsp;'MAST3',&nbsp;'FLOT1',&nbsp;'RPL11',&nbsp;'Gm10494',&nbsp;'1007_s_at',&nbsp;'AK125780']

上面的 xli 列表包含了 symbols, reporters 和 accession numbers，现在我们想要找回 Entrez gene id 和 uniprot id。幸运的是，mygene 的参数范围，字段，物种都足够灵活，可以支持多个值，列表或逗号分隔的字符串：

>>>&nbsp;mg.querymany(xli,&nbsp;scopes='symbol,reporter,accession',&nbsp;fields='entrezgene,uniprot',&nbsp;species='human')querying&nbsp;1-8...done.Finished.1&nbsp;input&nbsp;query&nbsp;terms&nbsp;found&nbsp;dup&nbsp;hits:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;[('1007_s_at',&nbsp;2)]2&nbsp;input&nbsp;query&nbsp;terms&nbsp;found&nbsp;no&nbsp;hit:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;['DDX26B',&nbsp;'Gm10494']Pass&nbsp;"returnall=True"&nbsp;to&nbsp;return&nbsp;complete&nbsp;lists&nbsp;of&nbsp;duplicate&nbsp;or&nbsp;missing&nbsp;query&nbsp;terms.[{'query':&nbsp;'DDX26B',&nbsp;'notfound':&nbsp;True},&nbsp;&nbsp;{'query':&nbsp;'CCDC83',&nbsp;'_id':&nbsp;'220047',&nbsp;'_score':&nbsp;88.13916,&nbsp;'entrezgene':&nbsp;'220047',&nbsp;'uniprot':&nbsp;{'Swiss-Prot':&nbsp;'Q8IWF9',&nbsp;'TrEMBL':&nbsp;'H0YDV3'}},&nbsp;&nbsp;{'query':&nbsp;'MAST3',&nbsp;'_id':&nbsp;'23031',&nbsp;'_score':&nbsp;88.42681,&nbsp;'entrezgene':&nbsp;'23031',&nbsp;'uniprot':&nbsp;{'Swiss-Prot':&nbsp;'O60307',&nbsp;'TrEMBL':&nbsp;'V9GYV0'}},&nbsp;&nbsp;{'query':&nbsp;'FLOT1',&nbsp;'_id':&nbsp;'10211',&nbsp;'_score':&nbsp;90.16039,&nbsp;'entrezgene':&nbsp;'10211',&nbsp;'uniprot':&nbsp;{'Swiss-Prot':&nbsp;'O75955',&nbsp;'TrEMBL':&nbsp;['A2AB09',&nbsp;'Q5ST80',&nbsp;'A2ABJ5',&nbsp;'A2AB10',&nbsp;'A2AB12',&nbsp;'A2AB13',&nbsp;'A2AB11']}},&nbsp;&nbsp;{'query':&nbsp;'RPL11',&nbsp;'_id':&nbsp;'6135',&nbsp;'_score':&nbsp;82.44751,&nbsp;'entrezgene':&nbsp;'6135',&nbsp;'uniprot':&nbsp;{'Swiss-Prot':&nbsp;'P62913',&nbsp;'TrEMBL':&nbsp;['Q5VVC8',&nbsp;'Q5VVD0',&nbsp;'A0A2R8Y447']}},&nbsp;&nbsp;{'query':&nbsp;'Gm10494',&nbsp;'notfound':&nbsp;True},&nbsp;&nbsp;{'query':&nbsp;'1007_s_at',&nbsp;'_id':&nbsp;'100616237',&nbsp;'_score':&nbsp;12.442588,&nbsp;'entrezgene':&nbsp;'100616237'},&nbsp;&nbsp;{'query':&nbsp;'1007_s_at',&nbsp;'_id':&nbsp;'780',&nbsp;'_score':&nbsp;11.8290205,&nbsp;'entrezgene':&nbsp;'780',&nbsp;'uniprot':&nbsp;{'Swiss-Prot':&nbsp;'Q08345',&nbsp;'TrEMBL':&nbsp;['A0A0A0MSX3',&nbsp;'A0A024RCL1',&nbsp;'A0A024RCQ1',&nbsp;'A0A024RCJ0',&nbsp;'Q96T61',&nbsp;'Q96T62',&nbsp;'A2ABM8',&nbsp;'A2ABL2',&nbsp;'A2ABL0',&nbsp;'E7ERN0',&nbsp;'A0A0G2JIA2',&nbsp;'D6RB35',&nbsp;'A0A0G2JI85',&nbsp;'D6RAJ3',&nbsp;'A0A0G2JHK4',&nbsp;'A0A0G2JJA0',&nbsp;'H0YAH6',&nbsp;'A0A140T972',&nbsp;'E7EUD5',&nbsp;'E7EXB0',&nbsp;'E7EPN2',&nbsp;'E7ETI3',&nbsp;'E7EVT1',&nbsp;'E7EVW6',&nbsp;'A0A0G2JNZ7',&nbsp;'H0Y717',&nbsp;'E7ESR9',&nbsp;'D6R9C4',&nbsp;'E7EQ23',&nbsp;'E7EUP7',&nbsp;'E7EQ30',&nbsp;'E7EPH4',&nbsp;'H0Y9F4',&nbsp;'E7EN94',&nbsp;'D6RBU7',&nbsp;'D6RGW5',&nbsp;'D6RB82',&nbsp;'E7ETX3',&nbsp;'E7EX99',&nbsp;'E7ERI6',&nbsp;'E7ES06',&nbsp;'E7ENJ2']}},&nbsp;&nbsp;{'query':&nbsp;'AK125780',&nbsp;'_id':&nbsp;'2978',&nbsp;'_score':&nbsp;10.087812,&nbsp;'entrezgene':&nbsp;'2978',&nbsp;'uniprot':&nbsp;{'Swiss-Prot':&nbsp;'P43080',&nbsp;'TrEMBL':&nbsp;['A6PVH5',&nbsp;'B2R9P6',&nbsp;'A0A0A0MTF5']}}]

从上一个结果中，你可能已经注意到查询词 "1007_s_at" 与两个基因匹配。在这种情况下，我们将从输出中收到通知，返回的结果将包括两个匹配的基因。

通过传递 "returnall = True"，我们将从返回的结果中获得重复或缺少的查询条目以及匹配的输出：

>>>&nbsp;mg.querymany(xli,&nbsp;scopes='symbol,reporter,accession',&nbsp;fields='entrezgene,uniprot',&nbsp;species='human',&nbsp;returnall=True)querying&nbsp;1-8...done.Finished.1&nbsp;input&nbsp;query&nbsp;terms&nbsp;found&nbsp;dup&nbsp;hits:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;[('1007_s_at',&nbsp;2)]2&nbsp;input&nbsp;query&nbsp;terms&nbsp;found&nbsp;no&nbsp;hit:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;['DDX26B',&nbsp;'Gm10494']{'out':&nbsp;[{'query':&nbsp;'DDX26B',&nbsp;'notfound':&nbsp;True},&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;{'query':&nbsp;'CCDC83',&nbsp;'_id':&nbsp;'220047',&nbsp;'_score':&nbsp;88.13916,&nbsp;'entrezgene':&nbsp;'220047',&nbsp;'uniprot':&nbsp;{'Swiss-Prot':&nbsp;'Q8IWF9',&nbsp;'TrEMBL':&nbsp;'H0YDV3'}},&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;{'query':&nbsp;'MAST3',&nbsp;'_id':&nbsp;'23031',&nbsp;'_score':&nbsp;88.42681,&nbsp;'entrezgene':&nbsp;'23031',&nbsp;'uniprot':&nbsp;{'Swiss-Prot':&nbsp;'O60307',&nbsp;'TrEMBL':&nbsp;'V9GYV0'}},&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;{'query':&nbsp;'FLOT1',&nbsp;'_id':&nbsp;'10211',&nbsp;'_score':&nbsp;90.20853,&nbsp;'entrezgene':&nbsp;'10211',&nbsp;'uniprot':&nbsp;{'Swiss-Prot':&nbsp;'O75955',&nbsp;'TrEMBL':&nbsp;['A2AB09',&nbsp;'Q5ST80',&nbsp;'A2ABJ5',&nbsp;'A2AB10',&nbsp;'A2AB12',&nbsp;'A2AB13',&nbsp;'A2AB11']}},&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;{'query':&nbsp;'RPL11',&nbsp;'_id':&nbsp;'6135',&nbsp;'_score':&nbsp;82.584694,&nbsp;'entrezgene':&nbsp;'6135',&nbsp;'uniprot':&nbsp;{'Swiss-Prot':&nbsp;'P62913',&nbsp;'TrEMBL':&nbsp;['Q5VVC8',&nbsp;'Q5VVD0',&nbsp;'A0A2R8Y447']}},&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;{'query':&nbsp;'Gm10494',&nbsp;'notfound':&nbsp;True},&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;{'query':&nbsp;'1007_s_at',&nbsp;'_id':&nbsp;'100616237',&nbsp;'_score':&nbsp;12.392551,&nbsp;'entrezgene':&nbsp;'100616237'},&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;{'query':&nbsp;'1007_s_at',&nbsp;'_id':&nbsp;'780',&nbsp;'_score':&nbsp;11.8290205,&nbsp;'entrezgene':&nbsp;'780',&nbsp;'uniprot':&nbsp;{'Swiss-Prot':&nbsp;'Q08345',&nbsp;'TrEMBL':&nbsp;['A0A0A0MSX3',&nbsp;'A0A024RCL1',&nbsp;'A0A024RCQ1',&nbsp;'A0A024RCJ0',&nbsp;'Q96T61',&nbsp;'Q96T62',&nbsp;'A2ABM8',&nbsp;'A2ABL2',&nbsp;'A2ABL0',&nbsp;'E7ERN0',&nbsp;'A0A0G2JIA2',&nbsp;'D6RB35',&nbsp;'A0A0G2JI85',&nbsp;'D6RAJ3',&nbsp;'A0A0G2JHK4',&nbsp;'A0A0G2JJA0',&nbsp;'H0YAH6',&nbsp;'A0A140T972',&nbsp;'E7EUD5',&nbsp;'E7EXB0',&nbsp;'E7EPN2',&nbsp;'E7ETI3',&nbsp;'E7EVT1',&nbsp;'E7EVW6',&nbsp;'A0A0G2JNZ7',&nbsp;'H0Y717',&nbsp;'E7ESR9',&nbsp;'D6R9C4',&nbsp;'E7EQ23',&nbsp;'E7EUP7',&nbsp;'E7EQ30',&nbsp;'E7EPH4',&nbsp;'H0Y9F4',&nbsp;'E7EN94',&nbsp;'D6RBU7',&nbsp;'D6RGW5',&nbsp;'D6RB82',&nbsp;'E7ETX3',&nbsp;'E7EX99',&nbsp;'E7ERI6',&nbsp;'E7ES06',&nbsp;'E7ENJ2']}},&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;{'query':&nbsp;'AK125780',&nbsp;'_id':&nbsp;'2978',&nbsp;'_score':&nbsp;10.106351,&nbsp;'entrezgene':&nbsp;'2978',&nbsp;'uniprot':&nbsp;{'Swiss-Prot':&nbsp;'P43080',&nbsp;'TrEMBL':&nbsp;['A6PVH5',&nbsp;'B2R9P6',&nbsp;'A0A0A0MTF5']}}&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;],&nbsp;&nbsp;'dup':&nbsp;[('1007_s_at',&nbsp;2)],&nbsp;&nbsp;'missing':&nbsp;['DDX26B',&nbsp;'Gm10494']}

上面代码返回的结果包含了用于匹配输出的列表 "out"，用于缺少查询项（列表）的 "missing"，以及用于具有多个匹配（包括匹配数）查询项的 "dup"。

根据 mygene 的说法，mygene 可以支持大批量的列表 ID 转换。如传递一个大于 1000 ids 的 id 列表（即上面的xli），mygene 将一次批量映射 1000 个 ID，然后将所有结果连接起来。因此，从用户端来看，它与传递较短列表完全相同。同时我们不必担心 mygene 后端服务器的饱和。

mygene 是一款强大的基因 ID 匹配转换模块，以 MyGene.info 为后台也可以有更多的玩法，感兴趣的可以参考MyGene.info 的官方文档：http://docs.mygene.info/en/latest/index.html，也欢迎留言交流。

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