一个简单的python接口，用于从病毒主机db查询信息
BioVirusHost的Python项目详细描述
生物病毒宿主
一个简单的python接口，用于从病毒宿主db查询信息
需求声明
biovirushost是一个简单的python接口，用于从病毒宿主数据库查询信息。病毒宿主数据库提供病毒及其宿主信息的集合，它是目前最大的数据库see。 需要以一种简单的pythonic方式从病毒主机db访问信息，这对于收集有关病毒和主机的数据非常有用。biovirushost是一个允许连接到病毒主机db api并从中解析信息的包。 病毒宿主数据库不提供api文档或示例，因此biovirushost的开发是为了快速方便地连接、获取和解析信息。
依赖关系
1-生物疗法
2-熊猫
安装说明
使用pip
pipinstallBioVirusHost
注意：Python>；=3.7是必需的
贡献指南
对于bug和建议，最有效的方法是在github问题跟踪器上提出问题。 Github允许您对问题进行分类，以便我们知道它是错误报告、功能请求还是对作者的反馈。
如果希望对代码进行一些更改，则应提交pull request 如何创建拉取请求？documentation on pull requests
用法
示例1
按病毒学名搜索病毒宿主。
fromBioVirusHostimportBioVirusHostfori_resultinBioVirusHost.v_search(["Caprine parainfluenza virus 3","Human parainfluenza virus 1 strain Washington/1964","Human parainfluenza virus 4a"]):print(i_result)
输出
| Virus (species) name | Virus lineage | Host name | Host lineage |
|---|---|---|---|
| Caprine parainfluenza virus 3 [TAX:1529392] | Viruses; Riboviria; Negarnaviricota; Haploviricotina; Monjiviricetes; Mononegavirales; Paramyxoviridae; Orthoparamyxovirinae; Respirovirus; Bovine respirovirus 3 | Capra hircus [TAX:9925] | Eukaryota; Metazoa; Chordata; Craniata; Sarcopterygii; Mammalia; Laurasiatheria; Ruminantia; Pecora; Bovidae; Caprinae; Capra |
| Virus (species) name | Virus lineage | Host name | Host lineage |
|---|---|---|---|
| Human parainfluenza virus 1 strain Washington/1964 [TAX:188538] | Viruses; Riboviria; Negarnaviricota; Haploviricotina; Monjiviricetes; Mononegavirales; Paramyxoviridae; Orthoparamyxovirinae; Respirovirus; Human respirovirus 1 | Homo sapiens [TAX:9606] | Eukaryota; Metazoa; Chordata; Craniata; Sarcopterygii; Mammalia; Euarchontoglires; Primates; Haplorrhini; Simiiformes; Catarrhini; Hominoidea; Hominidae; Homininae; Homo |
| Virus (species) name | Virus lineage | Host name | Host lineage |
|---|---|---|---|
| Human parainfluenza virus 4a [TAX:11224] | Viruses; Riboviria; Negarnaviricota; Haploviricotina; Monjiviricetes; Mononegavirales; Paramyxoviridae; Rubulavirus; Human rubulavirus 4 | Homo sapiens [TAX:9606] | Eukaryota; Metazoa; Chordata; Craniata; Sarcopterygii; Mammalia; Euarchontoglires; Primates; Haplorrhini; Simiiformes; Catarrhini; Hominoidea; Hominidae; Homininae; Homo |
示例2
按宿主学名搜索病毒宿主。
fromBioVirusHostimportBioVirusHostfori_resultinBioVirusHost.h_search(["Abutilon","Abelmoschus manihot"]):print(i_result)
输出
| Virus (species) name | Virus lineage | Host name | Host lineage |
|---|---|---|---|
| Abutilon mosaic virus [TAX:10815] | Viruses; Geminiviridae; Begomovirus | Abutilon [TAX:3630] | Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Malvales; Malvaceae; Malvoideae |
| Abutilon mosaic Bolivia virus [TAX:932071] | Viruses; Geminiviridae; Begomovirus | Abutilon [TAX:3630] | Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Malvales; Malvaceae; Malvoideae |
| Abutilon golden mosaic Yucatan virus [TAX:1312723] | Viruses; Geminiviridae; Begomovirus; Abutilon golden mosaic virus | Abutilon permolle [TAX:1312722] | Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Malvales; Malvaceae; Malvoideae; Abutilon |
| Abutilon Brazil virus [TAX:665102] | Viruses; Geminiviridae; Begomovirus | Abutilon [TAX:3630] | Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Malvales; Malvaceae; Malvoideae |
| Virus (species) name | Virus lineage | Host name | Host lineage |
|---|---|---|---|
| Ageratum conyzoides symptomless alphasatellite [TAX:1705092] | Viruses; Alphasatellitidae; Geminialphasatellitinae; unclassified Begomovirus-associated alphasatellites | Abelmoschus manihot subsp. tetraphyllus [TAX:1610811] | Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Malvales; Malvaceae; Malvoideae; Abelmoschus; Abelmoschus manihot |
| Ageratum conyzoides symptomless alphasatellite [TAX:1705092] | Viruses; Alphasatellitidae; Geminialphasatellitinae; unclassified Begomovirus-associated alphasatellites | Abelmoschus manihot [TAX:183220] | Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Malvales; Malvaceae; Malvoideae; Abelmoschus |
示例3
按病毒税ID搜索病毒主机。
fromBioVirusHostimportBioVirusHostfori_resultinBioVirusHost.v_tax_search([443876,438782]):print(i_result)
输出
| Virus (species) name | Virus lineage | Host name | Host lineage |
|---|---|---|---|
| African swine fever virus Benin 97/1 [TAX:443876] | Viruses; Asfarviridae; Asfivirus; African swine fever virus | Potamochoerus larvatus [TAX:273792] | Eukaryota; Metazoa; Chordata; Craniata; Sarcopterygii; Mammalia; Laurasiatheria; Suina; Suidae; Potamochoerus |
| African swine fever virus Benin 97/1 [TAX:443876] | Viruses; Asfarviridae; Asfivirus; African swine fever virus | Phacochoerus aethiopicus [TAX:85517] | Eukaryota; Metazoa; Chordata; Craniata; Sarcopterygii; Mammalia; Laurasiatheria; Suina; Suidae; Phacochoerus |
| African swine fever virus Benin 97/1 [TAX:443876] | Viruses; Asfarviridae; Asfivirus; African swine fever virus | Phacochoerus africanus [TAX:41426] | Eukaryota; Metazoa; Chordata; Craniata; Sarcopterygii; Mammalia; Laurasiatheria; Suina; Suidae; Phacochoerus |
| African swine fever virus Benin 97/1 [TAX:443876] | Viruses; Asfarviridae; Asfivirus; African swine fever virus | Sus scrofa [TAX:9823] | Eukaryota; Metazoa; Chordata; Craniata; Sarcopterygii; Mammalia; Laurasiatheria; Suina; Suidae; Sus |
| African swine fever virus Benin 97/1 [TAX:443876] | Viruses; Asfarviridae; Asfivirus; African swine fever virus | Ornithodoros [TAX:6937] | Eukaryota; Metazoa; Arthropoda; Chelicerata; Arachnida; Acari; Parasitiformes; Ixodida; Ixodoidea; Argasidae |
| Virus (species) name | Virus lineage | Host name | Host lineage |
|---|---|---|---|
| Abaca bunchy top virus [TAX:438782] | Viruses; Nanoviridae; Babuvirus | Musa acuminata AAA Group [TAX:214697] | Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Liliopsida; Petrosaviidae; Zingiberales; Musaceae; Musa |
| Abaca bunchy top virus [TAX:438782] | Viruses; Nanoviridae; Babuvirus | Musa sp. [TAX:46838] | Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Liliopsida; Petrosaviidae; Zingiberales; Musaceae; Musa |
示例4
按主机税ID搜索病毒主机。
fromBioVirusHostimportBioVirusHostfori_resultinBioVirusHost.h_tax_search([183220,3630]):print(i_result)
输出
| Virus (species) name | Virus lineage | Host name | Host lineage |
|---|---|---|---|
| Ageratum conyzoides symptomless alphasatellite [TAX:1705092] | Viruses; Alphasatellitidae; Geminialphasatellitinae; unclassified Begomovirus-associated alphasatellites | Abelmoschus manihot subsp. tetraphyllus [TAX:1610811] | Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Malvales; Malvaceae; Malvoideae; Abelmoschus; Abelmoschus manihot |
| Ageratum conyzoides symptomless alphasatellite [TAX:1705092] | Viruses; Alphasatellitidae; Geminialphasatellitinae; unclassified Begomovirus-associated alphasatellites | Abelmoschus manihot [TAX:183220] | Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Malvales; Malvaceae; Malvoideae; Abelmoschus |
| Virus (species) name | Virus lineage | Host name | Host lineage |
|---|---|---|---|
| Abutilon mosaic virus [TAX:10815] | Viruses; Geminiviridae; Begomovirus | Abutilon [TAX:3630] | Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Malvales; Malvaceae; Malvoideae |
| Abutilon mosaic Bolivia virus [TAX:932071] | Viruses; Geminiviridae; Begomovirus | Abutilon [TAX:3630] | Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Malvales; Malvaceae; Malvoideae |
| Abutilon golden mosaic Yucatan virus [TAX:1312723] | Viruses; Geminiviridae; Begomovirus; Abutilon golden mosaic virus | Abutilon permolle [TAX:1312722] | Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Malvales; Malvaceae; Malvoideae; Abutilon |
| Abutilon Brazil virus [TAX:665102] | Viruses; Geminiviridae; Begomovirus | Abutilon [TAX:3630] | Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Malvales; Malvaceae; Malvoideae |
示例5
使用病毒谱系和特定主机高级搜索病毒主机
fromBioVirusHostimportBioVirusHostfori_resultinBioVirusHost.comp_query("phasianinae","adenoviridae"):print(i_result)
输出
| Virus (species) name | Virus lineage | Host name | Host lineage |
|---|---|---|---|
| Avirulent turkey hemorrhagic enteritis virus [TAX:318490] | Viruses; Adenoviridae; Siadenovirus; Turkey siadenovirus A | Phasianinae [TAX:9072] | Eukaryota; Metazoa; Chordata; Craniata; Sarcopterygii; Aves; Neognathae; Galloanserae; Galliformes; Phasianidae |
示例6
获取有关病毒或其宿主的详细信息。
这将返回：
1-如果宿主信息=false（默认），则数据帧包含有关病毒（仅）作为基因组类型的信息。
fromBioVirusHostimportBioVirusHostprint(BioVirusHost.more_info("318490","A.N.Other@example.com"))
2-数据帧的生成器对象包含有关主机的信息（仅当主机信息=t时）。
fromBioVirusHostimportBioVirusHostfori_resultinBioVirusHost.more_info("318490","A.N.Other@example.com",True):print(i_result)
输出
| 0 | 1 |
|---|---|
| Scientific Name | Phasianinae [TAX:9072] |
| Lineage | Eukaryota; Metazoa; Chordata; Craniata; Sarcopterygii; Aves; Neognathae; Galloanserae; Galliformes; Phasianidae |
| Evidence | Literature |
| Reference | PMID: 19386786 |
| Authors | "Beach NM |
| Title | Comparison of 12 turkey hemorrhagic enteritis virus isolates allows prediction of genetic factors affecting virulence. |
| Journal | J Gen Virol. 2009 Aug;90(Pt 8):1978-85. |
| 0 | 1 |
|---|---|
| Scientific Name | Meleagris gallopavo [TAX:9103] |
| Lineage | Eukaryota; Metazoa; Chordata; Craniata; Sarcopterygii; Aves; Neognathae; Galloanserae; Galliformes; Phasianidae; Meleagridinae; Meleagris |
| Evidence | Literature |
| Reference | PMID: 19386786 |
| Authors | "Beach NM |
| Title | Comparison of 12 turkey hemorrhagic enteritis virus isolates allows prediction of genetic factors affecting virulence. |
| Journal | J Gen Virol. 2009 Aug;90(Pt 8):1978-85. |
| DBLINKS | KEGG GENOME: T01523 |
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