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