PyPI 官网下载 | taxonomy_ranks-0.0.7.tar.gz

# taxonomy-ranks ## 1 Introduction To get taxonomy ranks information with ETE3 Python3 module (`http://etetoolkit.org/`) ## 2 Installation Make sure your `pip` is from Python3 $ which pip /Users/mengguanliang/soft/miniconda3/bin/pip then type $ pip install taxonomy_ranks There will be a command `taxaranks` created under the same directory where your `pip` command located. If 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`. ## 3 Usage $ taxaranks taxaranks <taxonomy_list> <outfile> The '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. ete3 package will automatically download the NCBI Taxonomy database during the first time using of this program. Once 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. ### using as a module A taxa_name may have more than one potential_taxid. >>>from taxonomy_ranks import TaxonomyRanks >>>rank_taxon = TaxonomyRanks(taxa_name) >>>rank_taxon.get_lineage_taxids_and_taxanames() >>>ranks = ('user_taxa', 'taxa_searched', 'superkingdom', 'kingdom', 'superphylum', 'phylum', 'subphylum', 'superclass', 'class', 'subclass', 'superorder', 'order', 'suborder', 'superfamily', 'family', 'subfamily', 'genus', 'subgenus', 'species') >>>for rank in ranks: >>> print(rank, rank_taxon.lineages[potential_taxid][rank]) ## 4 Example run $ taxaranks test.taxa test.taxa.out Input file `test.taxa`content: Spodoptera litura Pieris rapae Locusta migratoria Frankliniella occidentalis Marsupenaeus japonicus Penaeus monodon Result file `test.taxa.out` content: superkingdom kingdom superphylum phylum subphylum superclass class subclass superorder ordersuborder superfamily family subfamily genus subgenus species Eukaryota Metazoa NA Arthropoda Hexapoda NA NA Pterygota NA Lepidoptera Glossata Noctuoidea Noctuidae Amphipyrinae Spodoptera NA Spodoptera litura Eukaryota Metazoa NA Arthropoda Hexapoda NA NA Pterygota NA Lepidoptera Glossata Papilionoidea Pieridae Pierinae Pieris NA Pieris rapae Eukaryota Metazoa NA Arthropoda Hexapoda NA NA Pterygota NA Orthoptera Caelifera Acridoidea Acrididae Oedipodinae Locusta NA Locusta migratoria Eukaryota Metazoa NA Arthropoda Hexapoda NA NA Pterygota NA Thysanoptera Terebrantia Thripoidea Thripidae Thripinae Frankliniella NA Frankliniella occidentalis Eukaryota Metazoa NA Arthropoda Crustacea Multicrustacea NA Eumalacostraca Eucarida Decapoda Dendrobranchiata Penaeoidea Penaeidae NA Marsupenaeus NA Marsupenaeus japonicus Eukaryota Metazoa NA Arthropoda Crustacea Multicrustacea NA Eumalacostraca Eucarida Decapoda Dendrobranchiata Penaeoidea Penaeidae NA Penaeus NA Penaeus monodon ## 5 Problems ### Your HOME directory runs out of space when downloading and installing the NCBI Taxonomy database during the first time using of this program. The error message can be: sqlite3.OperationalEoor: disk I/O error This 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. *Solutions:* The solution is obvious. 1. create a directory somewhere else that have enough space left: $ mkdir /other/place/myetetoolkit 2. remove the directory `~/.etetoolkit` created by `ete3`: $ rm -rf ~/.etetoolkit 3. link your new directory to the HOME directory: $ ln -s /other/place/myetetoolkit ~/.etetoolkit 4. run the program again: $ taxaranks my_taxonomy_list outfile This way, ete3 should work as expected. ### Update the NCBI taxonomy database For more details, refer to `http://etetoolkit.org/docs/latest/tutorial/tutorial_ncbitaxonomy.html`. 1. open a console, and type $ python3 You will enter the Python3 command line status. 2. excute following commands in Python3 >from ete3 import NCBITaxa >ncbi = NCBITaxa() >ncbi.update_taxonomy_database() ## 6 Citations Currently, I have no plan to publish `taxonomy-ranks`. However, since `taxonomy-ranks` makes use of the `ete3` toolkit, you should cite it if you use `taxonomy-ranks` in your publications. ETE 3: Reconstruction, analysis and visualization of phylogenomic data. Jaime Huerta-Cepas, Francois Serra and Peer Bork. Mol Biol Evol 2016; doi: 10.1093/molbev/msw046 Please go to `http://etetoolkit.org/` for more details. ## 7 Author Guanliang MENG. linzhi2012 at gmail.com