Metadata-Version: 2.1
Name: BioVirusHost
Version: 1.0.1
Summary: A simple Python interface to query the information from Virus-Host DB
Home-page: https://github.com/AliYoussef96/BioVirusHost
Author: Ali Mostafa
Author-email: ali.mo.anwar@std.agr.cu.edu.eg
License: MIT
Description: 
        # BioVirusHost
        A simple Python interface to query the information from Virus-Host DB
        
        [![Build Status](https://travis-ci.com/AliYoussef96/BioVirusHost.svg?token=anJWscmB7RsxdzyhVx5B&branch=master)](https://travis-ci.com/AliYoussef96/BioVirusHost)
        [![Documentation Status](https://readthedocs.org/projects/biovirushost/badge/?version=latest)](https://biovirushost.readthedocs.io/en/latest/?badge=latest)
        
        # 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](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 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](https://github.com/AliYoussef96/BioVirusHost/pulls)
        How to create a Pull Request? [documentation on pull requests](https://help.github.com/en/articles/about-pull-requests)
        
        # Usage
        
        #### Example 1
        
        Search for virus hosts by virus scientific name.
        
        ```python
        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.
        
        ```python
        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.
        
        ```python
        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.
        
        ```python
        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
        
        ```python
        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). 
        
        ```python
        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.
        
        ```python
        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| 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
        
        
Platform: UNKNOWN
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.7.0
Description-Content-Type: text/markdown
