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

Project description

BioVirusHost

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

Build Status Documentation Status

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

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.

from BioVirusHost import BioVirusHost

for i_result in BioVirusHost.v_search(["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.

from BioVirusHost import BioVirusHost

for i_result in BioVirusHost.h_search(["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.

from BioVirusHost import BioVirusHost

for i_result in BioVirusHost.v_tax_search([443876,438782]):
    print (i_result)

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.

from BioVirusHost import BioVirusHost

for i_result in BioVirusHost.h_tax_search([183220,3630]):
    print (i_result)

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

from BioVirusHost import BioVirusHost

for i_result in BioVirusHost.comp_query("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).

from BioVirusHost import BioVirusHost

print (BioVirusHost.more_info("318490", "A.N.Other@example.com"))

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

from BioVirusHost import BioVirusHost

for i_result in BioVirusHost.more_info("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
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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