bayerstraits_16s 1.0.6

# 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

## 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`\
Warning: please keep the exactly same OTU IDs in your.otu.table and your.otu.seqs!

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