bio-alignment 0.0.9 → 0.1.0

checksums.yaml

@@ -1,7 +1,7 @@
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data/Gemfile

@@ -1,5 +1,6 @@
 source "http://rubygems.org"
 gem "bio-logger"
+gem "bio-bigbio"
 gem "bio", ">= 1.5.0"      # for translation tables, BioRuby compat and Newick parser
 
 # Add dependencies to develop your gem here.
@@ -7,6 +8,6 @@ gem "bio", ">= 1.5.0"      # for translation tables, BioRuby compat and Newick p
 group :development do
   gem "rake"
   gem "bio-bigbio"         # for reading FASTA files in tests
-  gem "cucumber"
-  gem "rspec"
+  # gem "cucumber" - disabled tests
+  # gem "rspec"
 end

data/LICENSE.txt

@@ -1,4 +1,4 @@
-Copyright (c) 2012-2016 Pjotr Prins
+Copyright (c) 2012-2017 Pjotr Prins
 
 Permission is hereby granted, free of charge, to any person obtaining
 a copy of this software and associated documentation files (the

data/README.md

@@ -36,6 +36,13 @@ Bio::BioAlignment
 document](https://github.com/pjotrp/bioruby-alignment/blob/master/doc/bio-alignment-design.md)
 for Ruby.
 
+## Installation
+
+Dependencies are bioruby, bio-bigbio and bio-logger gems. To run the
+tests you also need to install rspec and cucumber gems.
+
+Bundler is no longer used.
+
 ## Command line
 
 bio-alignment comes with a command line interface (CLI), which can apply a number
@@ -82,7 +89,7 @@ aligmment (note codon gaps are represented by '---')
 
   include Bio::BioAlignment
   aln = Alignment.new
-  fasta = FastaReader.new('codon-alignment.fa')
+fasta = FastaReader.new('codon-alignment.fa')
   fasta.each do | rec |
     aln << CodonSequence.new(rec.id, rec.seq)
   end
@@ -171,23 +178,9 @@ Enumerable).
 
 ### Pal2nal
 
-A protein (amino acid) to nucleotide alignment would first load
-the sequences
-
-```ruby
-  aln1 = Alignment.new
-  fasta1 = FastaWriter.new('aa-aln.fa')
-  aln1.rows.each do | row |
-    fasta1.write(row.id, row.to_aa.to_s)
-  end
-  aln2 = Alignment.new
-  fasta2 = FastaReader.new('nt.fa')
-  fasta2.each do | rec |
-    aln2 << Sequence.new(rec.id, rec.seq)
-  end
-```
-
-Writing a (simple) version of pal2nal would be something like
+A protein (amino acid) to nucleotide alignment would first load the
+sequences and align them.  Writing a (simple) version of pal2nal would
+be something like
 
 ```ruby
   fasta3 = FastaWriter.new('nt-aln.fa')
@@ -210,14 +203,17 @@ Writing a (simple) version of pal2nal would be something like
   end
 ```
 
-With amino acid aa_aln and nucleotide nt_aln loaded, the library
-version of pal2nal includes validation
+We included a version (of course). With amino acid aa_aln and
+nucleotide nt_aln loaded, the library version of pal2nal includes
+validation
 
 ```ruby
   aln = aa_aln.pal2nal(nt_aln, :codon_table => 3, :do_validate => true)
 ```
 
-resulting in the codon alignment.
+resulting in the codon alignment. A command line
+[pal2nal](./bin/pal2nal) is also available on installing the gem.
+
 
 ### Phylogeny
 
@@ -368,4 +364,4 @@ This Biogem is published at [#bio-alignment](http://biogems.info/index.html)
 
 ## Copyright
 
-Copyright (c) 2012-2016 Pjotr Prins. See LICENSE.txt for further details.
+Copyright (c) 2012-2017 Pjotr Prins. See LICENSE.txt for further details.

data/Rakefile

@@ -1,14 +1,6 @@
 # encoding: utf-8
 
 require 'rubygems'
-# require 'bundler'
-# begin
-#   Bundler.setup(:default, :development)
-# rescue Bundler::BundlerError => e
-#   $stderr.puts e.message
-#   $stderr.puts "Run `bundle install` to install missing gems"
-#   exit e.status_code
-# end
 require 'rake'
 
 require 'rspec/core'

data/VERSION

@@ -1 +1 @@
-0.0.9
+0.1.0

data/bin/pal2nal

@@ -0,0 +1,118 @@
+#!/usr/bin/env ruby
+#
+
+USAGE = """
+Simple Pal2Nal implementation
+
+Pal2Nal converts a multiple sequence alignment of proteins and the
+corresponding DNA (or mRNA) sequences into a codon-based DNA
+alignment. This version implements a simple 1-to-1 matching with use
+of a codon table and validation(!)
+
+The resulting codon-based DNA alignment can further be subjected to
+the calculation of synonymous (Ks) and non-synonymous (Ka)
+substitution rates and be fed into PAML.
+
+   pep.aln     Protein (AA) alignment
+   nuc.fasta   Nucleotide sequences
+
+Example:
+
+   ./bin/pal2nal test/data/fasta/codon/aa-alignment.fa test/data/fasta/codon/nt.fa
+"""
+
+gempath = File.dirname(File.dirname(__FILE__))
+$: << File.join(gempath,'lib')
+
+VERSION_FILENAME=File.join(gempath,'VERSION')
+version = File.new(VERSION_FILENAME).read.chomp
+
+if ARGV.size == 0
+  print USAGE
+end
+
+require 'optparse'
+require 'bio-alignment'
+require 'bigbio'
+
+include Bio::BioAlignment
+
+options = {show_help: false, codon_table: 1, validate: true}
+
+opts = OptionParser.new do |o|
+  o.banner = "Usage: #{File.basename($0)} pep.aln  nuc.fasta [options]"
+
+  o.on("--codon-table [int]", Integer, "Codon table (default 1)") do |ct|
+    options[:codon_table] = ct
+  end
+
+  o.on("--no-validate", "Validate codons") do |b|
+    options[:validate] = false
+  end
+
+  o.on("-q", "--quiet", "Run quietly") do |q|
+    options[:quiet] = true
+  end
+
+  o.on("-v","--verbose", "Run verbosely") do |v|
+    options[:verbose] = true
+  end
+
+  o.on("-d", "--debug", "Debug mode") do |v|
+    options[:debug] = true
+  end
+
+  o.separator ""
+  o.on_tail('-h', '--help', 'display this help and exit') do
+    options[:show_help] = true
+  end
+end
+
+begin
+  opts.parse!(ARGV)
+
+  $stderr.print "Pal2Nal #{version} (biogem Ruby #{RUBY_VERSION}) by Pjotr Prins 2017\n" if !options[:quiet]
+
+  if options[:show_help] or ARGV.size < 2
+    print opts
+    print USAGE
+    exit 1
+  end
+
+  $stderr.print "Options: ",options,"\n" if !options[:quiet]
+
+rescue OptionParser::InvalidOption => e
+  options[:invalid_argument] = e.message
+end
+
+aafn = ARGV.shift
+ntfn = ARGV.shift
+
+aa_aln = Alignment.new
+aa     = FastaReader.new(aafn)
+aa.each do | rec |
+  aa_aln << Sequence.new(rec.id, rec.seq)
+end
+nt_aln = Alignment.new
+nt     = FastaReader.new(ntfn)
+nt.each do | rec |
+  nt_aln << Sequence.new(rec.id, rec.seq)
+end
+
+pal2nal = aa_aln.pal2nal(nt_aln, :codon_table => options[:codon_table], :do_validate => options[:validate])
+
+LINELEN = 60
+offset = 0
+size   = pal2nal.first.seq.size * 3
+
+print "CLUSTAL W multiple sequence alignment\n"
+while size > 0
+  print "\n"
+  pal2nal.each do | seq |
+    print seq.id," "*(18-seq.id.size)
+    print seq.to_nt[offset..offset+LINELEN-1],"\n"
+  end
+  offset += LINELEN
+  size -= LINELEN
+end
+print "\n"

metadata

@@ -1,19 +1,20 @@
 --- !ruby/object:Gem::Specification
 name: bio-alignment
 version: !ruby/object:Gem::Version
-  version: 0.0.9
+  version: 0.1.0
 platform: ruby
 authors:
 - Pjotr Prins
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2016-10-11 00:00:00.000000000 Z
+date: 2017-10-10 00:00:00.000000000 Z
 dependencies: []
 description: 
 email: pjotr.public01@thebird.nl
 executables:
 - bio-alignment
+- pal2nal
 extensions: []
 extra_rdoc_files:
 - LICENSE.txt
@@ -30,6 +31,7 @@ files:
 - TODO
 - VERSION
 - bin/bio-alignment
+- bin/pal2nal
 - doc/bio-alignment-design.md
 - features/bioruby-feature.rb
 - features/bioruby.feature
@@ -109,7 +111,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.5.1
+rubygems_version: 2.6.8
 signing_key: 
 specification_version: 4
 summary: Support for multiple sequence alignments (MSA)