{
    "info": {
        "author": "Ali Mostafa",
        "author_email": "ali.mo.anwar@std.agr.cu.edu.eg",
        "bugtrack_url": null,
        "classifiers": [
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: MIT License",
            "Programming Language :: Python :: 3",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
        ],
        "description": "# BioVirusHost\nA simple Python interface to query the information from Virus-Host DB\n\n[![Build Status](https://travis-ci.com/AliYoussef96/BioVirusHost.svg?token=anJWscmB7RsxdzyhVx5B&branch=master)](https://travis-ci.com/AliYoussef96/BioVirusHost)\n[![Documentation Status](https://readthedocs.org/projects/biovirushost/badge/?version=latest)](https://biovirushost.readthedocs.io/en/latest/?badge=latest)\n\n# Statement of need\n\nBioVirusHost 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 ).\nThe 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.\nVirus-Host DB does not provide API documentation or examples, hence BioVirusHost was developed to connect, get, and parse information fast and easy.\n\n# Dependencies\n\n1- Biopython\n\n2- pandas\n\n# Installation Instructions\n\n**Using pip**\n\n```python\npip install BioVirusHost\n```\n\n**Note:** Python >=3.7 is required.\n\n# Contribution Guidelines\n\n\nFor bugs and suggestions, the most effective way is by raising an issue on the github issue tracker. \nGithub allows you to classify your issues so that we know if it is a bug report, feature request or feedback to the authors.\n\nIf you wish to contribute some changes to the code then you should submit a [pull request](https://github.com/AliYoussef96/BioVirusHost/pulls)\nHow to create a Pull Request? [documentation on pull requests](https://help.github.com/en/articles/about-pull-requests)\n\n# Usage\n\n#### Example 1\n\nSearch for virus hosts by virus scientific name.\n\n```python\nfrom BioVirusHost import BioVirusHost\n\nfor i_result in BioVirusHost.v_search([\"Caprine parainfluenza virus 3\",\"Human parainfluenza virus 1 strain Washington/1964\",\"Human parainfluenza virus 4a\"]):\n    print (i_result)\n```\n\n**output**\n\nVirus (species) name|Virus lineage|Host name|Host lineage\n|-------------------|-------------|---------|------------|\nCaprine 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\n\nVirus (species) name|Virus lineage|Host name|Host lineage\n|-------------------|-------------|---------|------------|\nHuman 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\n\nVirus (species) name|Virus lineage|Host name|Host lineage\n|-------------------|-------------|---------|------------|\nHuman 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\n\n\n#### Example 2\n\nSearch for virus hosts by host scientific name.\n\n```python\nfrom BioVirusHost import BioVirusHost\n\nfor i_result in BioVirusHost.h_search([\"Abutilon\",\"Abelmoschus manihot\"]):\n    print (i_result)\n```\n\n**output**\n\nVirus (species) name|Virus lineage|Host name|Host lineage\n|-------------------|-------------|---------|------------|\nAbutilon mosaic virus [TAX:10815]|Viruses; Geminiviridae; Begomovirus|Abutilon [TAX:3630]|Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Malvales; Malvaceae; Malvoideae\nAbutilon mosaic Bolivia virus [TAX:932071]|Viruses; Geminiviridae; Begomovirus|Abutilon [TAX:3630]|Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Malvales; Malvaceae; Malvoideae\nAbutilon 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\nAbutilon Brazil virus [TAX:665102]|Viruses; Geminiviridae; Begomovirus|Abutilon [TAX:3630]|Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Malvales; Malvaceae; Malvoideae\n\nVirus (species) name|Virus lineage|Host name|Host lineage\n|-------------------|-------------|---------|------------|\nAgeratum 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\nAgeratum conyzoides symptomless alphasatellite [TAX:1705092]|Viruses; Alphasatellitidae; Geminialphasatellitinae; unclassified Begomovirus-associated alphasatellites|Abelmoschus manihot [TAX:183220]|Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Malvales; Malvaceae; Malvoideae; Abelmoschus\n\n\n#### Example 3\n\nSearch for virus hosts by virus TAX id.\n\n```python\nfrom BioVirusHost import BioVirusHost\n\nfor i_result in BioVirusHost.v_tax_search([443876,438782]):\n    print (i_result)\n```\n\n**output**\n\nVirus (species) name|Virus lineage|Host name|Host lineage\n|-------------------|-------------|---------|------------|\nAfrican 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\nAfrican 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\nAfrican 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\nAfrican 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\nAfrican 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\n\nVirus (species) name|Virus lineage|Host name|Host lineage\n|-------------------|-------------|---------|------------|\nAbaca bunchy top virus [TAX:438782]|Viruses; Nanoviridae; Babuvirus|Musa acuminata AAA Group [TAX:214697]|Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Liliopsida; Petrosaviidae; Zingiberales; Musaceae; Musa\nAbaca bunchy top virus [TAX:438782]|Viruses; Nanoviridae; Babuvirus|Musa sp. [TAX:46838]|Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Liliopsida; Petrosaviidae; Zingiberales; Musaceae; Musa\n\n\n#### Example 4\n\nSearch for virus hosts by host tax id.\n\n```python\nfrom BioVirusHost import BioVirusHost\n\nfor i_result in BioVirusHost.h_tax_search([183220,3630]):\n    print (i_result)\n```\n\n**output**\n\nVirus (species) name|Virus lineage|Host name|Host lineage\n|-------------------|-------------|---------|------------|\nAgeratum 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\nAgeratum conyzoides symptomless alphasatellite [TAX:1705092]|Viruses; Alphasatellitidae; Geminialphasatellitinae; unclassified Begomovirus-associated alphasatellites|Abelmoschus manihot [TAX:183220]|Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Malvales; Malvaceae; Malvoideae; Abelmoschus\n\nVirus (species) name|Virus lineage|Host name|Host lineage\n|-------------------|-------------|---------|------------|\nAbutilon mosaic virus [TAX:10815]|Viruses; Geminiviridae; Begomovirus|Abutilon [TAX:3630]|Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Malvales; Malvaceae; Malvoideae\nAbutilon mosaic Bolivia virus [TAX:932071]|Viruses; Geminiviridae; Begomovirus|Abutilon [TAX:3630]|Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Malvales; Malvaceae; Malvoideae\nAbutilon 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\nAbutilon Brazil virus [TAX:665102]|Viruses; Geminiviridae; Begomovirus|Abutilon [TAX:3630]|Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Malvales; Malvaceae; Malvoideae\n\n\n#### Example 5\n\nAdvanced search for virus hosts using virus lineage and a specific host\n\n```python\nfrom BioVirusHost import BioVirusHost\n\nfor i_result in BioVirusHost.comp_query(\"phasianinae\",\"adenoviridae\"):\n    print (i_result)\n```\n\n**output**\n\nVirus (species) name|Virus lineage|Host name|Host lineage\n|-------------------|-------------|---------|------------|\nAvirulent 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\n\n\n#### Example 6\n\nGet more information about the virus or its host.\n\nThis will return:\n\n1- A data frame contains information about a virus (only) as genome type if host_info = False (default). \n\n```python\nfrom BioVirusHost import BioVirusHost\n\nprint (BioVirusHost.more_info(\"318490\", \"A.N.Other@example.com\"))\n```\n\n2- A generator object for Data frame(s) contains infromation about hosts (only), if host_info = T.\n\n```python\nfrom BioVirusHost import BioVirusHost\n\nfor i_result in BioVirusHost.more_info(\"318490\", \"A.N.Other@example.com\",True):\n    print (i_result)\n```\n**output**\n\n0|1\n|-------------------|-------------|\nScientific Name|Phasianinae [TAX:9072]\nLineage|Eukaryota; Metazoa; Chordata; Craniata; Sarcopterygii; Aves; Neognathae; Galloanserae; Galliformes; Phasianidae\nEvidence|Literature\nReference|PMID: 19386786\nAuthors|\"Beach NM| Duncan RB| Larsen CT| Meng XJ| Sriranganathan N| Pierson FW\"\nTitle|Comparison of 12 turkey hemorrhagic enteritis virus isolates allows prediction of genetic factors affecting virulence.\nJournal|J Gen Virol. 2009 Aug;90(Pt 8):1978-85.\n\n\n0|1\n|-------------------|----------\nScientific Name|Meleagris gallopavo [TAX:9103]\nLineage|Eukaryota; Metazoa; Chordata; Craniata; Sarcopterygii; Aves; Neognathae; Galloanserae; Galliformes; Phasianidae; Meleagridinae; Meleagris\nEvidence|Literature\nReference|PMID: 19386786\nAuthors|\"Beach NM| Duncan RB| Larsen CT| Meng XJ| Sriranganathan N| Pierson FW\"\nTitle|Comparison of 12 turkey hemorrhagic enteritis virus isolates allows prediction of genetic factors affecting virulence.\nJournal|J Gen Virol. 2009 Aug;90(Pt 8):1978-85.\nDBLINKS|KEGG GENOME: T01523",
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