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        "author": "Guanliang MENG",
        "author_email": "mengguanliang@genomics.cn",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 3 - Alpha",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
            "Operating System :: MacOS :: MacOS X",
            "Operating System :: Microsoft :: Windows",
            "Operating System :: POSIX :: Linux",
            "Programming Language :: Python :: 3",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": "# taxonomy-ranks\n\n## 1 Introduction\nTo get taxonomy ranks information with ETE3 Python3 module (`http://etetoolkit.org/`)\n\n## 2 Installation\n\nMake sure your `pip` is from Python3\n\n\t$ which pip\n\t/Users/mengguanliang/soft/miniconda3/bin/pip\n\t\nthen type\n\n    $ pip install taxonomy_ranks\n\nThere will be a command `taxaranks` created under the same directory where your `pip` command located.\n\n\nIf you want to learn more about Python3 and `pip`, please refer to `https://www.python.org/` and `https://docs.python.org/3/tutorial/venv.html?highlight=pip`.\n\n## 3 Usage\n\t\n\t$ taxaranks\n\n\ttaxaranks <taxonomy_list> <outfile>\n\t\n\tThe 'taxonomy_list' file can be a list of ncbi taxa id or species names (or higher ranks, e.g. Family, Order), or a mixture of them.\n\t\n\tete3 package will automatically download the NCBI Taxonomy database during the first time using of this program.\n\t\n\t\nOnce the NCBI Taxonomy database has been installed, there is no need to connect to the network any more, unless you want to update the database after a period of time, for this case, please go to `http://etetoolkit.org/docs/latest/tutorial/tutorial_ncbitaxonomy.html` for more details.\n\n### using as a module\n\nA taxa_name may have more than one potential_taxid.\n\n\t\t>>>from taxonomy_ranks import TaxonomyRanks\n\t    >>>rank_taxon = TaxonomyRanks(taxa_name)\n\t    >>>rank_taxon.get_lineage_taxids_and_taxanames()\n\t    >>>ranks = ('user_taxa', 'taxa_searched', 'superkingdom', 'kingdom', 'superphylum', 'phylum', 'subphylum', 'superclass', 'class', 'subclass', 'superorder', 'order', 'suborder', 'superfamily', 'family', 'subfamily', 'genus', 'subgenus', 'species')\n\t    >>>for rank in ranks:\n\t    >>>    print(rank, rank_taxon.lineages[potential_taxid][rank])\n\n## 4 Example\n\nrun \n\n\t$ taxaranks test.taxa test.taxa.out\n\nInput file `test.taxa`content:\n\t\n\tSpodoptera litura\n\tPieris rapae\n\tLocusta migratoria\n\tFrankliniella occidentalis\n\tMarsupenaeus japonicus\n\tPenaeus monodon\n\nResult file `test.taxa.out` content:\n\n\tsuperkingdom\tkingdom\tsuperphylum\tphylum\tsubphylum\tsuperclass\tclass\tsubclass\tsuperorder\tordersuborder\tsuperfamily\tfamily\tsubfamily\tgenus\tsubgenus\tspecies\n\tEukaryota\tMetazoa\tNA\tArthropoda\tHexapoda\tNA\tNA\tPterygota\tNA\tLepidoptera\tGlossata\tNoctuoidea\tNoctuidae\tAmphipyrinae\tSpodoptera\tNA\tSpodoptera litura\n\tEukaryota\tMetazoa\tNA\tArthropoda\tHexapoda\tNA\tNA\tPterygota\tNA\tLepidoptera\tGlossata\tPapilionoidea\tPieridae\tPierinae\tPieris\tNA\tPieris rapae\n\tEukaryota\tMetazoa\tNA\tArthropoda\tHexapoda\tNA\tNA\tPterygota\tNA\tOrthoptera\tCaelifera\tAcridoidea\tAcrididae\tOedipodinae\tLocusta\tNA\tLocusta migratoria\n\tEukaryota\tMetazoa\tNA\tArthropoda\tHexapoda\tNA\tNA\tPterygota\tNA\tThysanoptera\tTerebrantia\tThripoidea\tThripidae\tThripinae\tFrankliniella\tNA\tFrankliniella occidentalis\n\tEukaryota\tMetazoa\tNA\tArthropoda\tCrustacea\tMulticrustacea\tNA\tEumalacostraca\tEucarida\tDecapoda\tDendrobranchiata\tPenaeoidea\tPenaeidae\tNA\tMarsupenaeus\tNA\tMarsupenaeus japonicus\n\tEukaryota\tMetazoa\tNA\tArthropoda\tCrustacea\tMulticrustacea\tNA\tEumalacostraca\tEucarida\tDecapoda\tDendrobranchiata\tPenaeoidea\tPenaeidae\tNA\tPenaeus\tNA\tPenaeus monodon\n\n## 5 Problems\n### Your HOME directory runs out of space when downloading and installing the NCBI Taxonomy database during the first time using of this program.\n\nThe error message can be:\n\t\n\tsqlite3.OperationalEoor: disk I/O error\n\nThis is caused by `ete3` which will create a directory `~/.etetoolkit` to store the databse (ca. 500M), however, your HOME directory does not have enough space left.\n\n*Solutions:*    \nThe solution is obvious.   \n\n1. create a directory somewhere else that have enough space left:\n\n\t\t$ mkdir /other/place/myetetoolkit\n\n\n2. remove the directory `~/.etetoolkit`  created by `ete3`:\n\n\t\t$ rm -rf ~/.etetoolkit\n\t\n\n3. link your new directory to the HOME directory:\n\n\t\t$ ln -s /other/place/myetetoolkit ~/.etetoolkit\n\t\t\n4. run the program again:\n\n\t\t$ taxaranks my_taxonomy_list outfile\n\nThis way, ete3 should work as expected.\n\n\n### Update the NCBI taxonomy database\nFor more details, refer to `http://etetoolkit.org/docs/latest/tutorial/tutorial_ncbitaxonomy.html`.\n\n1. open a console, and type\n\t\n\t\t$ python3\n\n\tYou will enter the Python3 command line status.\n\n2. excute following commands in Python3\n\t\t\n\t\t>from ete3 import NCBITaxa\n\t\t>ncbi = NCBITaxa()\n\t\t>ncbi.update_taxonomy_database()\n\n\n## 6 Citations\nCurrently, I have no plan to publish `taxonomy-ranks`.\n\nHowever, since `taxonomy-ranks` makes use of the `ete3` toolkit, you should cite it if you use `taxonomy-ranks` in your publications. \n\n\tETE 3: Reconstruction, analysis and visualization of phylogenomic data.\n\tJaime Huerta-Cepas, Francois Serra and Peer Bork. \n\tMol Biol Evol 2016; doi: 10.1093/molbev/msw046\n\nPlease go to `http://etetoolkit.org/` for more details.\n\n## 7 Author\n\nGuanliang MENG. \n\nlinzhi2012 at gmail.com",
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