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

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