Metadata-Version: 1.1
Name: prophyle
Version: 0.1.0.6
Summary: ProPhyle metagenomic classifier
Home-page: https://github.com/karel-brinda/prophyle
Author: Karel Brinda, Kamil Salikhov, Simone Pignotti, Gregory Kucherov
Author-email: kbrinda@hsph.harvard.edu, salikhov.kamil@gmail.com, pignottisimone@gmail.com, gregory.kucherov@univ-mlv.fr
License: MIT
Description: ProPhyle - accurate and resource-frugal phylogeny-based metagenomic classification
        ==================================================================================
        
        
        .. image:: https://travis-ci.org/karel-brinda/prophyle.svg?branch=master
        	:target: https://travis-ci.org/karel-brinda/prophyle
        
        
        Getting started
        ---------------
        
        Prerequisities
        ~~~~~~~~~~~~~~
        
        * GCC 4.8+
        * ZLib
        * Python 3 with ete3 library
        * SamTools
        
        Recommended way of installation using Conda
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        Environment installation:
        
        .. code-block:: bash
        
        	conda create -y --name prophyle \
        		-c etetoolkit -c bioconda \
        		python==3.4 ete3 bitarray \
        		parallel blast samtools=1.3.1
        
        
        Environment activation:
        
        .. code-block:: bash
        
                source activate prophyle
        
        
        Compile all programs
        
        .. code-block:: bash
        
          make -C src
        
        
        Custom taxonomic trees
        ~~~~~~~~~~~~~~~~~~~~~~
        
        Use [`bin/build_taxonomic_tree.py`](bin/build_taxonomic_tree.py) to build custom taxonomic trees starting from your database's fasta indexes and taxonomy files ([`library/Taxonomy`](library/Taxonomy) for more information). Taxonomic identifiers are assigned to the sequences first, and then the tree is built using [ETE Toolkit](http://etetoolkit.org/) and saved as newick format 1. Necessary node attributes are:
        
         * `name`: unique node name (format n[0-9]\*)
         * `taxid`: unique taxonomic identifier
         * `seqname`: names of the sequences sharing the same taxid, separated by @
         * `fastapath`: paths of the sequences' fasta files, separated by @ (absolute or relative from the main directory of the repository)
         * `infasta_offset`: positions where each sequence starts inside the corresponding fasta files, separated by @
         * `base_len`: length of each sequence, separated by @
        
        Other optional attributes are `sci_name`, `named_lineage`, `lineage`, `rank` (more info [here](http://etetoolkit.org/docs/latest/tutorial/tutorial_ncbitaxonomy.html#automatic-tree-annotation-using-ncbi-taxonomy)).
        
Keywords: metagenomics classification NGS
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: License :: OSI Approved :: MIT License
