Metadata-Version: 2.1
Name: buty-phyl
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: # buty_phyl
        ## Introduction
        * buty_phyl infers traits by 16S
        * input: otu table (-t) and otu sequences (-s)
        * requirement: mafft
        * Optional: fasttree
        ![alt text](https://raw.githubusercontent.com/caozhichongchong/buty_phyl/master/Methodology.png)
        
        ## Install
        `pip install buty_phyl`\
        in preparation: `anaconda download caozhichongchong/buty_phyl`
        
        ## Availability
        in preparation: https://anaconda.org/caozhichongchong/buty_phyl
        
        https://pypi.org/project/buty_phyl
        
        ## How to use it
        1. test the buty_phyl\
        `buty_phyl --test`
        
        2. try your data\
        `buty_phyl -t your.otu.table -s your.otu.seqs`\
        `buty_phyl -t your.otu.table -s your.otu.seqs -top 2000`
        
        3. try different traits (default is butyrate production)\
        predicting butyrate production\
        `buty_phyl -t your.otu.table -s your.otu.seqs`\
        or\
        `buty_phyl -t your.otu.table -s your.otu.seqs --rt b`\
        predicting sulfate reduction\
        `buty_phyl -t your.otu.table -s your.otu.seqs --rt s`\
        predicting nitrate reduction\
        `buty_phyl -t your.otu.table -s your.otu.seqs --rt n`
        
        4. use your own traits\
        `buty_phyl -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), unknown bacteria (0.5), 
        and non-butyrate-producing bacteria (0.0).
        * `filename.infertraits.abu`: the total abundance of butyrate-producing bacteria.
        * `filename.infertraits.commensal.abu`: the total abundance of commensal butyrate-producing bacteria.
        * `filename.infertraits.pathogen.abu`: the total abundance of pathogenic butyrate-producing bacteria.
        * `filename.infertraits.otu_table`: the otu_table of butyrate-producing bacteria.
        * `filename.infertraits.commensal.otu_table`: the otu_table of commensal butyrate-producing bacteria.
        * `filename.infertraits.pathogen.otu_table`: the otu_table of pathogenic butyrate-producing bacteria.
        * `filename.bpbspecies.commensal.abu`: the abundance of commensal butyrate-producing species.
        * `filename.bpbspecies.pathogen.abu`: the abundance of pathogenic butyrate-producing species.
        
        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
Description-Content-Type: text/markdown
