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Inferring traits by 16S

Project description

buty_phyl

Introduction

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

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

Project details


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Files for buty-phyl, version 1.0.7
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