Metadata-Version: 2.1
Name: taxonomy-ranks
Version: 0.0.8
Summary: To get taxonomy ranks information with ETE3 from NCBI Taxonomy database.
Home-page: http://mengguanliang.com
Author: Guanliang MENG
Author-email: linzhi2012@gmail.com
License: UNKNOWN
Description: # 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
        
        
        
        
        
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
Classifier: Programming Language :: Python :: 3
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: POSIX :: Linux
Requires-Python: >=3
Description-Content-Type: text/markdown
