traits_finder

Introduction

• traits_finder searches and summarizes traits in genomes and metagenomes
• input: reference database and folder of genomes/metagenomes
• requirement: python >= 3.0, blast or hmm
• requirement: for hmm, you need to prepare the hmm database
• optional: diamond, bwa, hs-blastn, usearch, mafft, fasttree

Install

pip install traits_finder
in preparation: anaconda download caozhichongchong/traits_finder

latest version (unstable though)

git clone https://github.com/caozhichongchong/traits_finder.git
cd traits_finder
python setup.py build
python setup.py install

Availability

https://pypi.org/project/traits_finder

What do you need to prepare

1. your reference database (-db your.db), protein sequences (-dbf 1) or dna sequences (-dbf 2)
2. a mapping file of functions to each reference sequence (sequence function)
3. all genomes/metagenomes in a folder (-i your.input.folder)
4. suffix or file extension of your genomes/metagenomes, such as .fasta or .fastq (-fa your.input.genome/metagenome.format)
5. programs to run: blast for similarity search (-s 1 )or hmm for domain search (-s 2)
6. optional programs to speedup! diamond, hs-blastn (or usearch for 16S extracting), usearch (necessary for HGT and HGT_sum)
7. optional programs to look at sequence variants! bwa, mafft, fasttree

How to use it

Search traits: boring and slow...

Database installed in traits_finder: antibiotic resistant genes (-db ARG), butyrate producing genes (-db but)

1. search protein reference sequences in genomes (traits_finder genome) or mobile genetic elements (traits_finder mge) by similarity search
   traits_finder genome -db your.db -i your.input.folder -fa your.input.genome.format --orf your.input.orf.format --r your.output.folder --r16 your.output.folder.for.16s --u diamond --bp blastp -dbf 1 -s 1\

2. search protein reference sequences in metagenomes by similarity search
   traits_finder meta -db your.db -i your.input.folder -fa your.input.metagenomes.format --r your.output.folder --r16 your.output.folder.for.16s --u diamond --bp blastp -dbf 1 -s 1\

3. search dna reference sequences in genomes by similarity search
   traits_finder genome -db your.db -i your.input.folder -fa your.input.genome.format --orf your.input.orf.format --r your.output.folder --r16 your.output.folder.for.16s --u usearch.or.hs-blastn --bp blastn -dbf 2 -s 1\

4. search dba reference sequences in metagenomes by similarity search
   traits_finder meta -db your.db -i your.input.folder -fa your.input.metagenomes.format --r your.output.folder --r16 your.output.folder.for.16s --u usearch.or.hs-blastn --bp blastn -dbf 2 -s 1\

5. search protein reference sequences in genomes by hmm
   traits_finder genome -db your.db -i your.input.folder -fa your.input.genome.format --orf your.input.orf.format --r your.output.folder --r16 your.output.folder.for.16s --hmm hmmscan -dbf 1 -s 2\

6. search dna reference sequences in genomes by alignment
   traits_finder genome -db your.db -i your.input.folder -fa your.input.genome.format --orf your.input.orf.format --r your.output.folder --r16 your.output.folder.for.16s --u usearch.or.hs-blastn --bp blastn --bwa bwa -dbf 2 -s 1\

7. search dna reference sequences in metagenomes by alignment
   traits_finder meta -db your.db -i your.input.folder -fa your.input.metagenomes.format --r your.output.folder --r16 your.output.folder.for.16s --u usearch.or.hs-blastn --bp blastn --bwa bwa -dbf 2 -s 1\

Summarize results: cool and fast!

1. summarize traits in genome
   traits_finder sum_genome -db your.db -m function.mapping.your.db -i your.input.folder -fa your.input.genome.format --orf your.input.orf.format --r your.output.folder --r16 your.output.folder.for.16s\

2. summarize traits in metagenomes
   traits_finder sum_meta -db your.db -m function.mapping.your.db -i your.input.folder -fa your.input.metagenomes.format --r your.output.folder --r16 your.output.folder.for.16s --meta metadata.txt\

HGT finder and summarizing: cool and fast! (still-testing)

Results

Copyright

Copyright: An Ni Zhang, Prof. Eric Alm, Alm Lab in MIT
Citation: Not yet, coming soon!
Contact: anniz44@mit.edu