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
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
-
test the buty_phyl
buty_phyl --test
-
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
-
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
-
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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