Welcome to BioVirusHost’s documentation!

About Virus-Host DataBase.

Virus-Host is a database providing information for the virus and its hosts’ relationships. It covers viruses with only complete genomes stored in NCBI/RefSeq and GenBank whose accession numbers are listed in EBI Genomes. For more information see: https://www.genome.jp/virushostdb/note.html

For the number of viruses in the database and more statistics see : https://www.genome.jp/virushostdb/stat.html

Citation for the Database.

Mihara, T., Nishimura, Y., Shimizu, Y., Nishiyama, H., Yoshikawa, G., Uehara, H., Hingamp, P., Goto, S., and Ogata, H.; Linking virus genomes with host taxonomy. Viruses 8, 66 doi:10.3390/v8030066 (2016).

Statement of need

BioVirusHost is a simple Python interface to query the information from Virus-Host DB. Virus-Host DB provides a collection of viruses and their host information, and it is the biggest database for now ( see : https://www.genome.jp/virushostdb/stat.html ).

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 connecting 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.

Usage

Example 1

Search for virus hosts by virus scientific name.

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)

This will return generator object for Data frame(s) contains ( virus (species) name, virus lineage, hostname, and host lineage ).

Example 2

Search for virus hosts by host scientific name.

for i_result in BioVirusHost.h_search([“Abutilon”,”Abelmoschus manihot”]):
print (i_result)

This will return a generator object for Data frame(s) contains ( virus (species) name, virus lineage, hostname, and host lineage ).

Example 3

Search for virus hosts by virus TAX id.

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

This will return generator object for Data frame(s) contains ( virus (species) name, virus lineage, hostname, and host lineage ).

Example 4

Search for virus hosts by host tax id.

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

This will return a generator object for Data frame(s) contains ( virus (species) name, virus lineage, hostname, and host lineage ).

Example 5

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

for i_result in BioVirusHost.comp_query(“phasianinae”,”adenoviridae”):
print (i_result)

This will return a generator object for Data frame(s) contains ( virus (species) name, virus lineage, hostname, and host lineage ).

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).

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.

for i_result in BioVirusHost.more_info(“318490”, “A.N.Other@example.com”,True):
print (i_result)

Dependencies

  • pandas
  • Biopython

Installation

Using pip:

pip install BioVirusHost

Contribution Guidelines

To report bugs or seek support please open an issue on this repository. Contributions to the software are welcome; please open an issue for further discussion on github: .

Help

If you need more help please contact ali.mo.anwar@std.agr.cu.edu.eg.

License

MIT License

Copyright (c) 2019 AliYoussef96

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

BioVirusHost module

BioVirusHost.comp_query(host, virus_lineage)[source]

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

Parameters:
  • host (str) – target host name or tax id
  • virus_lineage (str) – virus lineage
Returns:

A generator object for Data frame(s) contains ( virus (species) name, virus lineage, host name, and host lineage )
Raises:
  • TypeError if argument (host) is not a str
  • TypeError if argument (virus_lineage) is not a str

Search for virus hosts by host scientific name

Parameters:v_query (list) – list of host(s) scientific name
Returns:A generator object for Data frame(s) contains ( virus (species) name, virus lineage, host name, and host lineage )
Raises:TypeError if argument (h_query) is not a list

Search for virus hosts by host tax id

Parameters:tax_query (list) – list of host(s) tax id
Returns:A generator object for Data frame(s) contains ( virus (species) name, virus lineage, host name, and host lineage )
Raises:TypeError if argument (tax_query) is not a list
BioVirusHost.more_info(v_query, email, host_info=False)[source]

Get more information about the virus or its host

Parameters:
  • v_query (str or int) – target virus name or tax id
  • email (str) – your email address, required by the NCBI server
  • host_info (bool) – default = False
Returns:

A dataframe contains information about a virus (only) as genome type, if host_info = False (default)

A generator object for Data frame(s) contains infromation about hosts (only), if host_info = True
Raises:
  • TypeError if argument (v_query) is not a str
  • TypeError if argument (email) is not a str

Search for virus hosts by virus scientific name

Parameters:v_query (list) – list of virus(es) scientific name
Returns:A generator object for Data frame(s) contains ( virus (species) name, virus lineage, host name, and host lineage )
Raises:TypeError if argument (v_quer) is not a list

Search for virus hosts by virus TAX id

Parameters:tax_query (list) – list of virus(s) TAX id
Returns:A generator object for Data frame(s) contains ( virus (species) name, virus lineage, host name, and host lineage )
Raises:TypeError if argument (tax_query) is not a list

Indices and tables