bacterial-annotator 0.5.6 → 0.6.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/bin/ba_cdhit +51 -0
- data/bin/ba_diamond +46 -0
- data/bin/ba_fasta36 +47 -0
- data/bin/ba_fasttree +42 -0
- data/bin/ba_prodigal +2 -1
- data/bin/bacterial-annotator +13 -9
- data/lib/bacterial-annotator/sequence-synteny.rb +8 -1
- data/lib/bacterial-comparator.rb +18 -11
- metadata +10 -2
checksums.yaml
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SHA1:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 1ef156f21da883b7175715d94f734fe2cadb3d02
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data.tar.gz: 2620a56039162760e875242c1225bac333d78be1
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 44d3900f5b482a0bf66b87662384553603b7862d8c85b10c6eb71c498df18b9aba98fc792f590601faf6b50f03d638786b8e6515b05dc9444ef15c44412f1824
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data.tar.gz: dc65c44722a63fc21b3a87a3bad9770942788eb16da89d3c79d4a1ec154a095fa0304465fe1c5e5f076b8c57d04d8cddb765492678e48e212d4f32a805ddb52f
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data/bin/ba_cdhit
ADDED
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#!/usr/bin/env ruby
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# -*- coding: utf-8 -*-
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# author: maxime déraspe
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# email: maximilien1er@gmail.com
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# review:
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# date: 17-08-24
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# version: 0.01
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# licence:
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require 'open-uri'
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ROOT_path = File.dirname(__FILE__)
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# cdhit URL = "https://github.com/weizhongli/cdhit/releases/download/V4.6.8/cd-hit-v4.6.8-2017-0621-source.tar.gz"
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# Install cdhit on the user system
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def installcdhit
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begin
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resp = open("https://github.com/weizhongli/cdhit/releases/download/V4.6.8/cd-hit-v4.6.8-2017-0621-source.tar.gz")
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open("#{ROOT_path}/cdhit-4.6.8.tar.gz", "wb") do |file|
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file.write(resp.read)
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end
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Dir.chdir("#{ROOT_path}/")
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`tar xvf cdhit-4.6.8.tar.gz; rm cdhit-4.6.8.tar.gz`
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Dir.chdir("#{ROOT_path}/cd-hit-v4.6.8-2017-0621")
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`make`
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Dir.chdir("../")
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`mv ./cd-hit-v4.6.8-2017-0621/cd-hit ./cdhit.linux`
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`mv ./cd-hit-v4.6.8-2017-0621/cd-hit-2d ./cdhit2d.linux`
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File.chmod(0755, "#{ROOT_path}/cdhit.linux")
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File.chmod(0755, "#{ROOT_path}/cdhit2d.linux")
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rescue
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abort "Problem installing cdhit, aborting"
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end
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end
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# Install cdhit if not already install
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if ! File.exists? "#{ROOT_path}/cdhit.linux"
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puts "Installing cd-hit tools.."
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puts "Requirements: SSE+ instructions, OpenMP"
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puts "See https://github.com/weizhongli/cdhit/"
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puts "The Licence is GPLv2"
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installcdhit
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puts "cd-hit successfully installed in #{ROOT_path}/cdhit.linux and cdhit2d.linux"
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puts ""
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end
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data/bin/ba_diamond
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#!/usr/bin/env ruby
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# -*- coding: utf-8 -*-
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# author: maxime déraspe
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# email: maximilien1er@gmail.com
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# review:
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# date: 17-08-24
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# version: 0.01
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# licence:
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require 'open-uri'
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ROOT_path = File.dirname(__FILE__)
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# diamond URL = "https://github.com/bbuchfink/diamond/releases/download/v0.9.10/diamond-linux64.tar.gz"
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# Install diamond on the user system
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def installDiamond
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begin
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resp = open("https://github.com/bbuchfink/diamond/releases/download/v0.9.10/diamond-linux64.tar.gz")
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open("#{ROOT_path}/diamond-linux64.tar.gz", "wb") do |file|
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file.write(resp.read)
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end
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Dir.chdir("#{ROOT_path}/")
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`tar xvf diamond-linux64.tar.gz; rm diamond-linux64.tar.gz`
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`mv diamond ./diamond.linux`
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`rm diamond_manual.pdf`
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File.chmod(0755, "#{ROOT_path}/diamond.linux")
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rescue
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abort "Problem installing Diamond, aborting"
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end
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end
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# Install diamond if not already install
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if ! File.exists? "#{ROOT_path}/diamond.linux"
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puts "Installing Diamond aligner.."
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puts "See https://github.com/bbuchfink/diamond/"
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puts "The Licence is GPLv3"
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installDiamond
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puts "Diamond successfully installed in #{ROOT_path}/diamond.linux"
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puts ""
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end
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data/bin/ba_fasta36
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#!/usr/bin/env ruby
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# -*- coding: utf-8 -*-
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# author: maxime déraspe
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# email: maximilien1er@gmail.com
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# review:
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# date: 17-08-24
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# version: 0.01
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# licence:
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require 'open-uri'
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ROOT_path = File.dirname(__FILE__)
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# fasta36 URL = "https://github.com/wrpearson/fasta36/releases/download/v36.3.8d_13Apr16/fasta-36.3.8d-linux64.tar.gz"
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# Install fasta36 on the user system
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def installFasta36
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begin
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resp = open("https://github.com/wrpearson/fasta36/releases/download/v36.3.8d_13Apr16/fasta-36.3.8d-linux64.tar.gz")
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open("#{ROOT_path}/fasta-36.3.8d-linux64.tar.gz", "wb") do |file|
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file.write(resp.read)
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end
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Dir.chdir("#{ROOT_path}/")
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`tar xvf fasta-36.3.8d-linux64.tar.gz; rm fasta-36.3.8d-linux64.tar.gz`
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`cp fasta-36.3.8d/bin/fasta36 ./fasta36.linux`
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`cp fasta-36.3.8d/bin/glsearch36 ./glsearch36.linux`
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`cp fasta-36.3.8d/bin/tfastx36 ./tfastx36.linux`
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File.chmod(0755, "#{ROOT_path}/fasta36.linux")
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rescue
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abort "Problem installing Fasta36, aborting"
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end
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end
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# Install fasta36 if not already install
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if ! File.exists? "#{ROOT_path}/fasta36.linux"
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puts "Installing Fasta36 aligner.."
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puts "See https://github.com/wrpearson/fasta36/"
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puts "The Licence is Apache 2"
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installFasta36
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puts "Fasta36 successfully installed in #{ROOT_path}/fasta36.linux"
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puts ""
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end
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data/bin/ba_fasttree
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#!/usr/bin/env ruby
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# -*- coding: utf-8 -*-
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# author: maxime déraspe
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# email: maximilien1er@gmail.com
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# review:
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# date: 15-02-24
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# version: 0.01
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# licence:
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require 'open-uri'
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ROOT_path = File.dirname(__FILE__)
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# fasttree_url = http://www.microbesonline.org/fasttree/FastTreeMP
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# Install FASTTREE on the user system
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def installFastTree
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begin
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resp = open("http://www.microbesonline.org/fasttree/FastTreeMP")
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open("#{ROOT_path}/fasttree.linux", "wb") do |file|
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file.write(resp.read)
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end
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Dir.chdir("#{ROOT_path}/")
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File.chmod(0755, "#{ROOT_path}/fasttree.linux")
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rescue
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abort "Problem in stalling FastTree, aborting"
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end
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end
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# Install prodigal if not already install
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if ! File.exists? "#{ROOT_path}/fasttree.linux"
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puts "Installing FastTree .."
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puts "See http://www.microbesonline.org/fasttree/#Install"
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puts "License - OpenSource (unknown)"
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installFastTree
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puts "FastTree successfully installed in #{ROOT_path}/fasttree.linux"
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puts ""
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end
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data/bin/ba_prodigal
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`tar xvf v2.6.2.tar.gz; rm v2.6.2.tar.gz`
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Dir.chdir("#{ROOT_path}/Prodigal-2.6.2")
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`make`
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Dir.chdir("../")
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`cp Prodigal-2.6.2/prodigal prodigal.linux`
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File.chmod(0755, "#{ROOT_path}/prodigal.linux")
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# Dir.chir("#{ROOT_path}")
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# File.chmod(0755, "#{ROOT_path}/prodigal.linux")
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data/bin/bacterial-annotator
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--input/-i <fasta_file> Provide the fasta file to annotate
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--outdir/-o <outdir> Output directory [default=BAnnotation]
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--force/-f Force to overwrite the output directory
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--name/-n <name> Sample name
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//
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--
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--guessref Will guess the best reference genome to use for the annotation.
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// MERGEM-based Annotation (Recommended)
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--db MERGEM database directory
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// Reference-Based Annotation
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--refgenome/-g <GBK_ID> Provide a Genbank file or a Gbk Accession ID.
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--externaldb <proteins fasta_file>
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Finish or do a complete annotation with this sequence database (a protein fasta file).
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Fasta headers need to look similar to NCBI or EBI fasta headers, ex.:
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>gi|385721352|gb|AFI72857.1| NDM-1 [Escherichia coli]
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>sp|C7C422|BLAN1_KLEPN Beta-lactamase NDM-1 OS=Klebsiella pneumoniae..
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-
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// Other options
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--pidentity <% identity> Minimum percentage identity to incorporate a CDS annotation [default=0.7]
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--pcoverage <% identity> Minimum percentage of coverage over protein alignment to incorporate a CDS annotation [default=0.7]
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.. otherwise hint for a non-functional protein
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-
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--minlength <length> Minimum contig length for annotation [default=500]
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--meta Better for metagenome and plasmid annotations because of disparate codon usage [default=off]
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--align [dna|prot|both] by default align only proteins
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--concat <nb of genes> by default 0=all
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//Phylogeny (
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//Phylogeny (Maximum Likelihood)
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--phylogeny will build phylogenetic tree from the alignments files (pep or dna)
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--
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--software [raxml|fasttree] (default fasttree)
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--bootstrap <nb of bootstrap> (default 100)
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OEM
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@@ -197,11 +197,15 @@ if ARGV.size > 1
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ROOT = File.dirname(__FILE__)
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# Check for 3rd party dependencies : Prodigal, Blat, MAFFT
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# Check for 3rd party dependencies : Prodigal, Blat, MAFFT, ...
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system("ba_prodigal")
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system("ba_blat")
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system("ba_mafft")
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system("ba_raxml")
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system("ba_diamond")
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system("ba_fasta36")
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system("ba_cdhit")
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system("ba_fasttree")
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options = {}
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genomes_list = [] # TODO multiple input genomes
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@@ -35,6 +35,13 @@ class SequenceSynteny
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flat.each_entry do |s|
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s_name = s.definition.chomp.split(" ")[0]
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sequences[s_name] = {}
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properties = s.definition.chomp.split(";")
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partial = false
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if properties.length >= 2 and properties[1].include? "partial"
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partial = (properties[1].gsub("partial=","")=='01')
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puts "partial:" + partial.to_s
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end
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sequences[s_name][:partial] = partial
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sequences[s_name][:length] = s.seq.length
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sequences[s_name][:conserved] = false
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sequences[s_name][:contig] = s_name.split("_")[0..-2].join("_") if s_name.include? "_"
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@@ -88,7 +95,7 @@ class SequenceSynteny
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assert_cutoff = [1,1,1]
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assert_cutoff[0] = 0 if lA[2].to_f < @pidentity
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assert_cutoff[1] = 0 if cov_query < @min_coverage
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-
assert_cutoff[2] = 0 if cov_subject < @min_coverage
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assert_cutoff[2] = 0 if cov_subject < @min_coverage and @query_sequences[key][:partial] == false
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# first hit for query
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if ! @query_sequences[key].has_key? :homology
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data/lib/bacterial-comparator.rb
CHANGED
|
@@ -24,7 +24,6 @@ class BacterialComparator
|
|
|
24
24
|
@genomes_list = options[:genomes_list]
|
|
25
25
|
@proc = options[:proc].to_i
|
|
26
26
|
@phylo_nb_genes = options[:phylo_nb_genes]
|
|
27
|
-
|
|
28
27
|
min_cov = options[:min_cov].to_f
|
|
29
28
|
min_pid = options[:pidentity].to_f
|
|
30
29
|
if min_cov > 1
|
|
@@ -209,7 +208,7 @@ class BacterialComparator
|
|
|
209
208
|
else
|
|
210
209
|
status = "OK"
|
|
211
210
|
status = "FAILED" if cmd != true
|
|
212
|
-
puts "Alignment #{f} : #{status}"
|
|
211
|
+
# puts "Alignment #{f} : #{status}"
|
|
213
212
|
end
|
|
214
213
|
rescue
|
|
215
214
|
if trying < 3
|
|
@@ -248,7 +247,11 @@ class BacterialComparator
|
|
|
248
247
|
puts "..Prot alignment files already exists, skipping."
|
|
249
248
|
end
|
|
250
249
|
|
|
251
|
-
|
|
250
|
+
# ugly hack to find out the reference genome
|
|
251
|
+
ref_id = Dir["#{ori_dir}/#{@genomes_list[0]}/*.pep"][0].split('/')[-1].gsub(".pep","")
|
|
252
|
+
|
|
253
|
+
concat_alignments "align-genes-pep.all.fasta", ref_id
|
|
254
|
+
|
|
252
255
|
Dir.chdir(ori_dir)
|
|
253
256
|
|
|
254
257
|
end
|
|
@@ -277,13 +280,17 @@ class BacterialComparator
|
|
|
277
280
|
puts "..Gene alignment files already exists, skipping."
|
|
278
281
|
end
|
|
279
282
|
|
|
280
|
-
|
|
283
|
+
# ugly hack to find out the reference genome
|
|
284
|
+
ref_id = Dir["#{ori_dir}/#{@genomes_list[0]}/*.pep"][0].split('/')[-1].gsub(".pep","")
|
|
285
|
+
|
|
286
|
+
concat_alignments "align-genes-dna.all.fasta", ref_id
|
|
287
|
+
|
|
281
288
|
Dir.chdir(ori_dir)
|
|
282
289
|
|
|
283
290
|
end
|
|
284
291
|
|
|
285
292
|
|
|
286
|
-
def concat_alignments outfile
|
|
293
|
+
def concat_alignments outfile, ref_id
|
|
287
294
|
|
|
288
295
|
if File.exists?("../#{outfile}") and File.size("../#{outfile}") > 0
|
|
289
296
|
puts "..Alignment concatenated file already exists, skipping."
|
|
@@ -292,8 +299,6 @@ class BacterialComparator
|
|
|
292
299
|
|
|
293
300
|
fout = File.open("../#{outfile}", "w")
|
|
294
301
|
|
|
295
|
-
ref_id = Dir["../../#{@genomes_list[0]}/*.pep"][0].gsub(/.*\//,"").gsub(".pep","")
|
|
296
|
-
|
|
297
302
|
seq = ""
|
|
298
303
|
Dir["*.aln"].each do |f|
|
|
299
304
|
flat = Bio::FlatFile.auto(f)
|
|
@@ -303,7 +308,7 @@ class BacterialComparator
|
|
|
303
308
|
end
|
|
304
309
|
|
|
305
310
|
bioseq = Bio::Sequence.auto(seq)
|
|
306
|
-
out = bioseq.output_fasta("#{ref_id}",60)
|
|
311
|
+
out = bioseq.output_fasta("#{ref_id}", 60)
|
|
307
312
|
fout.write(out)
|
|
308
313
|
|
|
309
314
|
for i in 1..@genomes_list.length
|
|
@@ -325,7 +330,9 @@ class BacterialComparator
|
|
|
325
330
|
flat.close
|
|
326
331
|
end
|
|
327
332
|
bioseq = Bio::Sequence.auto(seq)
|
|
328
|
-
|
|
333
|
+
# get the file name without path prefix and extension
|
|
334
|
+
genome_name = genomes_list[i-1].split("/")[-1].split(".")[0]
|
|
335
|
+
out = bioseq.output_fasta(genome_name,60)
|
|
329
336
|
fout.write(out)
|
|
330
337
|
end
|
|
331
338
|
|
|
@@ -358,7 +365,7 @@ class BacterialComparator
|
|
|
358
365
|
tree_dir = "#{current_dir}/tree-genes-dna"
|
|
359
366
|
cmd = system("#{@root}/raxml.linux -T #{@proc} -f d -N #{bt} -s align-genes-dna.all.fasta -m GTRGAMMA -p 123454321 -n DnaTree -w #{tree_dir}")
|
|
360
367
|
cmd = system("cat #{tree_dir}/RAxML_result.DnaTree.RUN.* >> #{tree_dir}/RAxML_result.BS")
|
|
361
|
-
cmd = system("#{@root}/raxml.linux -T
|
|
368
|
+
cmd = system("#{@root}/raxml.linux -T #{@proc} -f b -z #{tree_dir}/RAxML_result.BS -t #{tree_dir}/RAxML_bestTree.DnaTree -m GTRGAMMA -n DNA_BS_TREE -w #{tree_dir}")
|
|
362
369
|
cmd = system("ln -s #{tree_dir}/RAxML_bipartitionsBranchLabels.DNA_BS_TREE #{tree_dir}/../")
|
|
363
370
|
Dir.chdir(ori_dir)
|
|
364
371
|
end
|
|
@@ -374,7 +381,7 @@ class BacterialComparator
|
|
|
374
381
|
tree_dir = "#{current_dir}/tree-genes-pep"
|
|
375
382
|
cmd = system("#{@root}/raxml.linux -T #{@proc} -f d -N #{bt} -s align-genes-pep.all.fasta -m PROTGAMMAAUTO -p 123454321 -n PepTree -w #{tree_dir}")
|
|
376
383
|
cmd = system("cat #{tree_dir}/RAxML_result.PepTree.RUN.* >> #{tree_dir}/RAxML_result.BS")
|
|
377
|
-
cmd = system("#{@root}/raxml.linux -T
|
|
384
|
+
cmd = system("#{@root}/raxml.linux -T #{@proc} -f b -z #{tree_dir}/RAxML_result.BS -t #{tree_dir}/RAxML_bestTree.PepTree -m PROTGAMMAAUTO -n PEP_BS_TREE -w #{tree_dir}")
|
|
378
385
|
cmd = system("ln -s #{tree_dir}/RAxML_bipartitionsBranchLabels.PEP_BS_TREE #{tree_dir}/../")
|
|
379
386
|
Dir.chdir(ori_dir)
|
|
380
387
|
|
metadata
CHANGED
|
@@ -1,14 +1,14 @@
|
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
|
2
2
|
name: bacterial-annotator
|
|
3
3
|
version: !ruby/object:Gem::Version
|
|
4
|
-
version: 0.
|
|
4
|
+
version: 0.6.0
|
|
5
5
|
platform: ruby
|
|
6
6
|
authors:
|
|
7
7
|
- Maxime Deraspe
|
|
8
8
|
autorequire:
|
|
9
9
|
bindir: bin
|
|
10
10
|
cert_chain: []
|
|
11
|
-
date: 2017-
|
|
11
|
+
date: 2017-09-18 00:00:00.000000000 Z
|
|
12
12
|
dependencies:
|
|
13
13
|
- !ruby/object:Gem::Dependency
|
|
14
14
|
name: bio
|
|
@@ -79,10 +79,18 @@ executables:
|
|
|
79
79
|
- ba_blat
|
|
80
80
|
- ba_mafft
|
|
81
81
|
- ba_raxml
|
|
82
|
+
- ba_diamond
|
|
83
|
+
- ba_fasta36
|
|
84
|
+
- ba_cdhit
|
|
85
|
+
- ba_fasttree
|
|
82
86
|
extensions: []
|
|
83
87
|
extra_rdoc_files: []
|
|
84
88
|
files:
|
|
85
89
|
- bin/ba_blat
|
|
90
|
+
- bin/ba_cdhit
|
|
91
|
+
- bin/ba_diamond
|
|
92
|
+
- bin/ba_fasta36
|
|
93
|
+
- bin/ba_fasttree
|
|
86
94
|
- bin/ba_mafft
|
|
87
95
|
- bin/ba_prodigal
|
|
88
96
|
- bin/ba_raxml
|