BlastLCA

This is a julia package to identify lowest common ancestor (LCA) from blast results.

It requires

Blast result (include qseqid, bitscore, pidents and staxids)
NCBI Taxonomy database (see Taxonomy.jl)

This tool is referred to Carradec et al., 2018. See Methods section (Taxonomic assignment).

Example

using BlastLCA
using Taxonomy

db = Taxonomy.DB("/db/taxonomy/nodes.dmp", "/db/taxonomy/names.dmp")

blastout_path = "your_blast_result.txt"

minimal = 0.90
cutoff = 0.67
precision = Dict{Symbol, Float64}(
    :class => 0.50,
    :order => 0.65,
    :family => 0.80,
    :genus => 0.95,
    :species => 1.0)

ranks = [:superkingdom, :phylum, :class, :order, :family, :genus, :species]

f = x-> weightedLCA(x, minimal, cutoff, ranks, precision)

blastLCA(diamond_path, "lca_output_path.txt";
               taxonomy=db,
               method=f,
               header=false,
               qseqid_pos=1,
               staxids_pos=13,
               pident_pos=3,
               bitscore_pos=12
               );

CLI

This package also supports CLI.

Install

julia -e "import Pkg; Pkg.add(url=\"https://github.com/banhbio/BlastLCA.jl\")"

export PATH="~/.julia/bin:$PATH"
#or
ln -s ~/.julia/bin/blastlca /where/in/PATH

Usage

blastlca -h
blastlca weighted -h

Run weighted LCA

balstlca wighted /your/blastresult.tsv -o output.tsv --nodes-path /db/nodes.dmp --names-path /db/names.dmp