bacterial-annotator 0.5.6 → 0.6.0
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- 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
CHANGED
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@@ -1,7 +1,7 @@
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1
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---
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SHA1:
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-
metadata.gz:
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data.tar.gz:
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3
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metadata.gz: 1ef156f21da883b7175715d94f734fe2cadb3d02
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4
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data.tar.gz: 2620a56039162760e875242c1225bac333d78be1
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5
5
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SHA512:
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6
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metadata.gz:
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-
data.tar.gz:
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6
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metadata.gz: 44d3900f5b482a0bf66b87662384553603b7862d8c85b10c6eb71c498df18b9aba98fc792f590601faf6b50f03d638786b8e6515b05dc9444ef15c44412f1824
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7
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data.tar.gz: dc65c44722a63fc21b3a87a3bad9770942788eb16da89d3c79d4a1ec154a095fa0304465fe1c5e5f076b8c57d04d8cddb765492678e48e212d4f32a805ddb52f
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data/bin/ba_cdhit
ADDED
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@@ -0,0 +1,51 @@
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1
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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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6
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# date: 17-08-24
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# version: 0.01
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8
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# licence:
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require 'open-uri'
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11
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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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20
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open("#{ROOT_path}/cdhit-4.6.8.tar.gz", "wb") do |file|
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21
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file.write(resp.read)
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22
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end
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23
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Dir.chdir("#{ROOT_path}/")
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24
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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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26
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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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30
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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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40
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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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50
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end
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51
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data/bin/ba_diamond
ADDED
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@@ -0,0 +1,46 @@
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1
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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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5
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# review:
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6
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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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44
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45
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end
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46
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data/bin/ba_fasta36
ADDED
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@@ -0,0 +1,47 @@
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1
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#!/usr/bin/env ruby
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2
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# -*- coding: utf-8 -*-
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3
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# author: maxime déraspe
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4
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# email: maximilien1er@gmail.com
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5
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# review:
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6
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# date: 17-08-24
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7
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# version: 0.01
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8
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# licence:
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9
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10
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require 'open-uri'
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ROOT_path = File.dirname(__FILE__)
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13
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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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14
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15
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# Install fasta36 on the user system
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def installFasta36
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18
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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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22
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+
end
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23
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Dir.chdir("#{ROOT_path}/")
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24
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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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25
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`cp fasta-36.3.8d/bin/fasta36 ./fasta36.linux`
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26
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`cp fasta-36.3.8d/bin/glsearch36 ./glsearch36.linux`
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27
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`cp fasta-36.3.8d/bin/tfastx36 ./tfastx36.linux`
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28
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+
File.chmod(0755, "#{ROOT_path}/fasta36.linux")
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29
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+
rescue
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30
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+
abort "Problem installing Fasta36, aborting"
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31
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+
end
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32
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+
|
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33
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+
end
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34
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35
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36
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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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38
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puts "Installing Fasta36 aligner.."
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40
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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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42
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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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45
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46
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end
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47
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data/bin/ba_fasttree
ADDED
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@@ -0,0 +1,42 @@
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1
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#!/usr/bin/env ruby
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2
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# -*- coding: utf-8 -*-
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3
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# author: maxime déraspe
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4
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# email: maximilien1er@gmail.com
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5
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# review:
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6
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# date: 15-02-24
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7
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# version: 0.01
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8
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# licence:
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9
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10
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require 'open-uri'
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11
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ROOT_path = File.dirname(__FILE__)
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13
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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
CHANGED
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@@ -24,7 +24,8 @@ def installProdigal
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`tar xvf v2.6.2.tar.gz; rm v2.6.2.tar.gz`
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25
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Dir.chdir("#{ROOT_path}/Prodigal-2.6.2")
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`make`
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-
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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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30
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# Dir.chir("#{ROOT_path}")
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31
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# File.chmod(0755, "#{ROOT_path}/prodigal.linux")
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data/bin/bacterial-annotator
CHANGED
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@@ -44,22 +44,21 @@ annotate [OPTIONS]
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44
44
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--input/-i <fasta_file> Provide the fasta file to annotate
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45
45
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--outdir/-o <outdir> Output directory [default=BAnnotation]
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46
46
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--force/-f Force to overwrite the output directory
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47
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+
--name/-n <name> Sample name
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47
48
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48
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-
//
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49
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-
--
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50
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-
--guessref Will guess the best reference genome to use for the annotation.
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49
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// MERGEM-based Annotation (Recommended)
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50
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--db MERGEM database directory
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51
51
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52
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+
// Reference-Based Annotation
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53
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+
--refgenome/-g <GBK_ID> Provide a Genbank file or a Gbk Accession ID.
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52
54
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--externaldb <proteins fasta_file>
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53
55
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Finish or do a complete annotation with this sequence database (a protein fasta file).
|
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54
56
|
Fasta headers need to look similar to NCBI or EBI fasta headers, ex.:
|
|
55
57
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>gi|385721352|gb|AFI72857.1| NDM-1 [Escherichia coli]
|
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56
58
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>sp|C7C422|BLAN1_KLEPN Beta-lactamase NDM-1 OS=Klebsiella pneumoniae..
|
|
57
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-
|
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58
|
-
// Other options
|
|
59
59
|
--pidentity <% identity> Minimum percentage identity to incorporate a CDS annotation [default=0.7]
|
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60
60
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--pcoverage <% identity> Minimum percentage of coverage over protein alignment to incorporate a CDS annotation [default=0.7]
|
|
61
61
|
.. otherwise hint for a non-functional protein
|
|
62
|
-
|
|
63
62
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--minlength <length> Minimum contig length for annotation [default=500]
|
|
64
63
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|
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65
64
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--meta Better for metagenome and plasmid annotations because of disparate codon usage [default=off]
|
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@@ -131,9 +130,10 @@ compare [OPTIONS]
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131
130
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--align [dna|prot|both] by default align only proteins
|
|
132
131
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--concat <nb of genes> by default 0=all
|
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133
132
|
|
|
134
|
-
//Phylogeny (
|
|
133
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+
//Phylogeny (Maximum Likelihood)
|
|
135
134
|
--phylogeny will build phylogenetic tree from the alignments files (pep or dna)
|
|
136
|
-
--
|
|
135
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+
--software [raxml|fasttree] (default fasttree)
|
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136
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+
--bootstrap <nb of bootstrap> (default 100)
|
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137
137
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|
|
138
138
|
OEM
|
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139
139
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@@ -197,11 +197,15 @@ if ARGV.size > 1
|
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197
197
|
|
|
198
198
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ROOT = File.dirname(__FILE__)
|
|
199
199
|
|
|
200
|
-
# Check for 3rd party dependencies : Prodigal, Blat, MAFFT
|
|
200
|
+
# Check for 3rd party dependencies : Prodigal, Blat, MAFFT, ...
|
|
201
201
|
system("ba_prodigal")
|
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202
202
|
system("ba_blat")
|
|
203
203
|
system("ba_mafft")
|
|
204
204
|
system("ba_raxml")
|
|
205
|
+
system("ba_diamond")
|
|
206
|
+
system("ba_fasta36")
|
|
207
|
+
system("ba_cdhit")
|
|
208
|
+
system("ba_fasttree")
|
|
205
209
|
|
|
206
210
|
options = {}
|
|
207
211
|
genomes_list = [] # TODO multiple input genomes
|
|
@@ -35,6 +35,13 @@ class SequenceSynteny
|
|
|
35
35
|
flat.each_entry do |s|
|
|
36
36
|
s_name = s.definition.chomp.split(" ")[0]
|
|
37
37
|
sequences[s_name] = {}
|
|
38
|
+
properties = s.definition.chomp.split(";")
|
|
39
|
+
partial = false
|
|
40
|
+
if properties.length >= 2 and properties[1].include? "partial"
|
|
41
|
+
partial = (properties[1].gsub("partial=","")=='01')
|
|
42
|
+
puts "partial:" + partial.to_s
|
|
43
|
+
end
|
|
44
|
+
sequences[s_name][:partial] = partial
|
|
38
45
|
sequences[s_name][:length] = s.seq.length
|
|
39
46
|
sequences[s_name][:conserved] = false
|
|
40
47
|
sequences[s_name][:contig] = s_name.split("_")[0..-2].join("_") if s_name.include? "_"
|
|
@@ -88,7 +95,7 @@ class SequenceSynteny
|
|
|
88
95
|
assert_cutoff = [1,1,1]
|
|
89
96
|
assert_cutoff[0] = 0 if lA[2].to_f < @pidentity
|
|
90
97
|
assert_cutoff[1] = 0 if cov_query < @min_coverage
|
|
91
|
-
assert_cutoff[2] = 0 if cov_subject < @min_coverage
|
|
98
|
+
assert_cutoff[2] = 0 if cov_subject < @min_coverage and @query_sequences[key][:partial] == false
|
|
92
99
|
|
|
93
100
|
# first hit for query
|
|
94
101
|
if ! @query_sequences[key].has_key? :homology
|
data/lib/bacterial-comparator.rb
CHANGED
|
@@ -24,7 +24,6 @@ class BacterialComparator
|
|
|
24
24
|
@genomes_list = options[:genomes_list]
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25
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@proc = options[:proc].to_i
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26
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@phylo_nb_genes = options[:phylo_nb_genes]
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27
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-
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27
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min_cov = options[:min_cov].to_f
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29
28
|
min_pid = options[:pidentity].to_f
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29
|
if min_cov > 1
|
|
@@ -209,7 +208,7 @@ class BacterialComparator
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208
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else
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209
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status = "OK"
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|
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210
|
status = "FAILED" if cmd != true
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|
-
puts "Alignment #{f} : #{status}"
|
|
211
|
+
# puts "Alignment #{f} : #{status}"
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212
|
end
|
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213
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rescue
|
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215
214
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if trying < 3
|
|
@@ -248,7 +247,11 @@ class BacterialComparator
|
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|
248
247
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puts "..Prot alignment files already exists, skipping."
|
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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
|