buty-phyl 1.0.6

Inferring traits by 16S

buty_phyl

Introduction

• buty_phyl infers traits by 16S
• input: otu table (-t) and otu sequences (-s)
• requirement: mafft
• Optional: fasttree

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: [e-mail]