BioVirusHost

A simple Python interface to query the information from Virus-Host DB

Statement of need

BioVirusHost is a simple Python interface to query information from Virus-Host database. Virus-Host DB provides a collection of viruses and their host information, and it is the biggest database present see. The need to access the information from the Virus-Host DB in a simple pythonic way is very useful for collecting data about viruses and hosts. BioVirusHost is a package that allows the connection to the Virus-Host DB API and parses information from it. Virus-Host DB does not provide API documentation or examples, hence BioVirusHost was developed to connect, get, and parse information fast and easy.

Dependencies

1- Biopython

2- pandas

Installation Instructions

Using pip

python pip install BioVirusHost

Note: Python >=3.7 is required.

Contribution Guidelines

For bugs and suggestions, the most effective way is by raising an issue on the github issue tracker. Github allows you to classify your issues so that we know if it is a bug report, feature request or feedback to the authors.

If you wish to contribute some changes to the code then you should submit a pull request How to create a Pull Request? documentation on pull requests

Usage

Example 1

Search for virus hosts by virus scientific name.

```python from BioVirusHost import BioVirusHost

for iresult in BioVirusHost.vsearch(["Caprine parainfluenza virus 3","Human parainfluenza virus 1 strain Washington/1964","Human parainfluenza virus 4a"]): print (i_result) ```

output

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

Example 2

Search for virus hosts by host scientific name.

```python from BioVirusHost import BioVirusHost

for iresult in BioVirusHost.hsearch(["Abutilon","Abelmoschus manihot"]): print (i_result) ```

output

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

Example 3

Search for virus hosts by virus TAX id.

```python from BioVirusHost import BioVirusHost

for iresult in BioVirusHost.vtaxsearch([443876,438782]): print (iresult) ```

output

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

Example 4

Search for virus hosts by host tax id.

```python from BioVirusHost import BioVirusHost

for iresult in BioVirusHost.htaxsearch([183220,3630]): print (iresult) ```

output

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

Example 5

Advanced search for virus hosts using virus lineage and a specific host

```python from BioVirusHost import BioVirusHost

for iresult in BioVirusHost.compquery("phasianinae","adenoviridae"): print (i_result) ```

output

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

Example 6

Get more information about the virus or its host.

This will return:

1- A data frame contains information about a virus (only) as genome type if host_info = False (default).

```python from BioVirusHost import BioVirusHost

for iresult in BioVirusHost.moreinfo("318490", "A.N.Other@example.com",False): print (i_result) ```

2- A generator object for Data frame(s) contains infromation about hosts (only), if host_info = T.

```python from BioVirusHost import BioVirusHost

for iresult in BioVirusHost.moreinfo("318490", "A.N.Other@example.com",True): print (i_result) ``` output

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| Duncan RB| Larsen CT| Meng XJ| Sriranganathan N| Pierson FW" 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| Duncan RB| Larsen CT| Meng XJ| Sriranganathan N| Pierson FW" 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

Citation

Ali Mostafa Anwar. (2019, August 14). BioVirusHost: A simple Python interface to query the information from Virus-Host DB (Version v1.0.1). Zenodo. http://doi.org/10.5281/zenodo.3368326