Metadata-Version: 1.1
Name: bayerstraits_16s
Version: 1.0.5
Summary: Inferring traits by 16S
Home-page: https://github.com/caozhichongchong/BayersTraits_16S
Author:: Anni Zhang
Author-email:: anniz44@mit.edu
License: MIT
Description: # bayerstraits_16s
        # This is a temp version of bayerstraits_16s
        ## Introduction
        * bayerstraits_16s infers traits by 16S
        * input: otu table (-t) and otu sequences (-s)
        * requirement: mafft
        * Optional: fasttree
        ![alt text](https://raw.githubusercontent.com/caozhichongchong/bayerstraits_16s/master/Methodology.png)
        
        ## Install
        `pip install bayerstraits_16s`\
        in preparation: `anaconda download caozhichongchong/bayerstraits_16s`
        
        ## Test (any of these two commands)
        `bayerstraits_16s --test`\
        `bayerstraits_16s -t your.otu.table -s your.otu.seqs`
        
        ## Availability
        in preparation: https://anaconda.org/caozhichongchong/bayerstraits_16s
        
        https://pypi.org/project/bayerstraits_16s
        
        ## How to use it
        1. test the bayerstraits_16s\
        `bayerstraits_16s --test`
        
        2. try your data\
        `bayerstraits_16s -t your.otu.table -s your.otu.seqs`\
        `bayerstraits_16s -t your.otu.table -s your.otu.seqs -top 2000`
        
        3. use your own traits\
        `bayerstraits_16s -t your.otu.table -s your.otu.seqs --rs your.own.reference.16s --rt your.own.reference.traits`
        
        * your.own.reference.16s is a fasta file containing the 16S sequences of your genomes\
        \>Genome_ID1\
        ATGC...\
        \>Genome_ID2\
        ATGC...
        
        * your.own.reference.traits is a metadata of whether there's trait in your genomes (0 for no and 1 for yes)\
        Genome_ID1   0\
        Genome_ID1   1
        
        ## Results
        The result dir of "Bayers_model":
        * `filename.infertraits.txt`: the OTUs inferring as butyrate-producing bacteria (1.0, 0.5) 
        and non-butyrate-producing bacteria (0.0).
        * `filename.infertraits.abu`: the total abundance of butyrate-producing bacteria in all samples.
        * `filename.infertraits.otu_table`: the otu_table of butyrate-producing bacteria in all samples.
        
        The result dir of "Filtered_OTU":
        * Some temp files of filtered OTUs, alignment, and tree.
        
        ## Copyright
        Copyright: An Ni Zhang, Prof. Eric Alm, Alm Lab in MIT\
        Citation: Not yet, coming soon!\
        Contact: anniz44@mit.edu
        
Keywords: 16S,bacterial genomes,function,traits
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
