ms-fasta 0.2.3 → 0.4.0
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- data/.gitignore +7 -0
- data/History +4 -0
- data/{MIT-LICENSE → LICENSE} +1 -0
- data/Rakefile +98 -0
- data/VERSION +1 -0
- data/lib/ms/fasta.rb +66 -2
- data/lib/ms/fasta/ipi.rb +31 -0
- data/lib/ms/fasta/ipi/dat.rb +14 -0
- data/spec/ms/fasta/archive_spec.rb +49 -0
- data/spec/ms/fasta/entry_spec.rb +86 -0
- data/spec/ms/fasta/ipi/dat_spec.rb +7 -0
- data/spec/ms/fasta/ipi_spec.rb +34 -0
- data/spec/ms/fasta_spec.rb +76 -0
- data/spec/spec_helper.rb +4 -0
- metadata +36 -44
data/.gitignore
ADDED
data/History
CHANGED
data/{MIT-LICENSE → LICENSE}
RENAMED
data/Rakefile
ADDED
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@@ -0,0 +1,98 @@
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require 'rubygems'
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require 'rake'
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require 'jeweler'
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require 'rake/testtask'
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require 'rcov/rcovtask'
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NAME = "ms-fasta"
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WEBSITE_BASE = "website"
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WEBSITE_OUTPUT = WEBSITE_BASE + "/output"
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gemspec = Gem::Specification.new do |s|
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s.name = NAME
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s.authors = ["John T. Prince"]
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s.email = "jtprince@gmail.com"
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s.homepage = "http://jtprince.github.com/" + NAME
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s.summary = "An mspire library for working with fasta formatted files"
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s.description = "provides programmatic access to fasta files"
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s.rubyforge_project = 'mspire'
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s.add_development_dependency("spec-more", ">= 1.1.0")
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end
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Jeweler::Tasks.new(gemspec)
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Rake::TestTask.new(:spec) do |spec|
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spec.libs << 'lib' << 'spec'
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spec.pattern = 'spec/**/*_spec.rb'
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spec.verbose = true
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end
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Rcov::RcovTask.new do |spec|
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spec.libs << 'spec'
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spec.pattern = 'spec/**/*_spec.rb'
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spec.verbose = true
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end
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def rdoc_redirect(base_rdoc_output_dir, package_website_page, version)
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content = %Q{
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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
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<html><head><title>mspire: } + NAME + %Q{rdoc</title>
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<meta http-equiv="REFRESH" content="0;url=#{package_website_page}/rdoc/#{version}/">
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</head> </html>
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}
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FileUtils.mkpath(base_rdoc_output_dir)
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File.open("#{base_rdoc_output_dir}/index.html", 'w') {|out| out.print content }
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end
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require 'rake/rdoctask'
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Rake::RDocTask.new do |rdoc|
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base_rdoc_output_dir = WEBSITE_OUTPUT + '/rdoc'
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version = File.read('VERSION')
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rdoc.rdoc_dir = base_rdoc_output_dir + "/#{version}"
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rdoc.title = NAME + ' ' + version
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rdoc.rdoc_files.include('README*')
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rdoc.rdoc_files.include('lib/**/*.rb')
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end
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task :create_redirect do
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base_rdoc_output_dir = WEBSITE_OUTPUT + '/rdoc'
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rdoc_redirect(base_rdoc_output_dir, gemspec.homepage,version)
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end
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task :rdoc => :create_redirect
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namespace :website do
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desc "checkout and configure the gh-pages submodule"
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task :init do
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if File.exist?(WEBSITE_OUTPUT + "/.git")
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puts "!! not doing anything, #{WEBSITE_OUTPUT + "/.git"} already exists !!"
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else
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puts "(not sure why this won't work programmatically)"
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puts "################################################"
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puts "[Execute these commands]"
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puts "################################################"
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puts "git submodule init"
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puts "git submodule update"
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puts "pushd #{WEBSITE_OUTPUT}"
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puts "git co --track -b gh-pages origin/gh-pages ;"
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puts "popd"
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puts "################################################"
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# not sure why this won't work!
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#%x{git submodule init}
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#%x{git submodule update}
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#Dir.chdir(WEBSITE_OUTPUT) do
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# %x{git co --track -b gh-pages origin/gh-pages ;}
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#end
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end
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end
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end
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task :default => :spec
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task :build => :gemspec
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98
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# credit: Rakefile modeled after Jeweler's
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data/VERSION
ADDED
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@@ -0,0 +1 @@
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1
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0.4.0
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data/lib/ms/fasta.rb
CHANGED
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@@ -2,15 +2,79 @@ require 'ms/fasta/archive'
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2
2
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3
3
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module Ms
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4
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module Fasta
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5
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VERSION = '0.2.3'
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-
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7
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def self.new(*args, &block)
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Ms::Fasta::Archive.new(*args, &block).reindex
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7
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end
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10
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9
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#def self.open(filename, &block)
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#Ms::Fasta::Archive.open(filename, 'rb', [], &block)
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#end
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12
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def self.open(*args, &block)
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Ms::Fasta::Archive.open(*args, &block)
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end
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14
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def self.foreach(*args, &block)
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Ms::Fasta::Archive.open(*args) do |fasta|
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fasta.each(&block)
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end
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21
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end
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22
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23
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# returns :ipi, :ncbi, or nil if can't be determined
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def self.filetype(file_or_io)
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ft = nil
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io =
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if file_or_io.is_a?(String)
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File.open(file_or_io)
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else
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init_pos = file_or_io.pos
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file_or_io.rewind
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file_or_io
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end
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34
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io.each_line do |line|
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35
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if line =~ /^>/
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36
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ft = header_to_filetype(line[1..-1])
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break
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38
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end
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end
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40
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if file_or_io.is_a?(String)
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io.close
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else
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44
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io.pos = init_pos
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45
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end
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46
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ft
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47
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end
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48
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49
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# takes the header line (no leading >) and returns the kind of file
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50
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def self.header_to_filetype(line)
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51
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if line =~ /^IPI\:/
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52
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:ipi
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53
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elsif line =~ /^gi\|/
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54
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:ncbi
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55
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else
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56
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nil
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57
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end
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end
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# kind is :ipi or :ncbi or a String (the header)
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# gives the regular expression for parsing the header (no leading >)
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62
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def self.id_regexp(kind)
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63
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sym =
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64
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if kind.is_a?(String)
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header_to_filetype(kind)
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else ; kind
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67
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end
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68
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case sym
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69
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when :ipi
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/^IPI:(.*?)\|/o
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71
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when :ncbi
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/^gi\|(.*?)\|/o
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else
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nil
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75
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end
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76
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end
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77
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15
78
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end
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16
79
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end
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80
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+
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data/lib/ms/fasta/ipi.rb
ADDED
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@@ -0,0 +1,31 @@
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1
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2
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module Ms
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3
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module Fasta
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4
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module Ipi
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5
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IPI_RE = /IPI:([\w\.]+)\|/o
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6
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class << self
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7
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# returns a hash of header information where the values are all
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8
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# strings (does NOT attempt to separate on ';'). The gene description
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9
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# is held in the key 'description'
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10
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def parse(header)
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11
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gap_index = header.index(' ')
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hash = {}
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13
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header[0...gap_index].split('|').each do |str|
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(key, val) = str.split(':')
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hash[key] = val
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16
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end
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17
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pieces = header[gap_index..-1].split(' ')
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hash.store(*pieces.shift.split('='))
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hash.store(*pieces.shift.split('='))
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hash.store('description', pieces.join(' '))
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hash
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22
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end
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23
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+
|
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24
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# returns the ipi index for the header (.e.g, ipi0000093.1)
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25
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def ipi(header)
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26
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IPI_RE.match(header)[1]
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27
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end
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28
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end
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29
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end
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end
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31
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end
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@@ -0,0 +1,49 @@
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require File.join(File.dirname(__FILE__), '../../spec_helper.rb')
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2
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require 'ms/fasta/archive'
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3
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4
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class FastaAchiveSpec
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5
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include Ms::Fasta
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6
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7
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describe 'fasta archive operations' do
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8
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9
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FASTA_0 = %Q{>gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus]
|
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10
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+
LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV
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11
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+
GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX
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+
IENY
|
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13
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}
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14
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+
|
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15
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FASTA_1 = %Q{>gi|1048576| protein sequence
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16
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+
PROTEIN
|
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17
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+
}
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18
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+
|
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19
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it 'reindexes' do
|
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20
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+
strio = StringIO.new(FASTA_0 + FASTA_1)
|
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21
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+
begin
|
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22
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+
a = Archive.new(strio)
|
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23
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+
|
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24
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+
a.length.is 0
|
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25
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+
a.reindex
|
|
26
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+
a.length.is 2
|
|
27
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+
|
|
28
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+
a[0].to_s.is FASTA_0
|
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29
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+
a[1].to_s.is FASTA_1
|
|
30
|
+
a[1].header.is "gi|1048576| protein sequence"
|
|
31
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+
ensure
|
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32
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+
a.close
|
|
33
|
+
end
|
|
34
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+
end
|
|
35
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+
|
|
36
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it 'properly converts the fasta string to an entry object' do
|
|
37
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+
begin
|
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38
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+
a = Archive.new
|
|
39
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+
e = a.str_to_entry(FASTA_0)
|
|
40
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+
|
|
41
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+
e.isa Entry
|
|
42
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+
e.header.is "gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus]"
|
|
43
|
+
e.sequence.is("LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV" + "GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX" + "IENY")
|
|
44
|
+
ensure
|
|
45
|
+
a.close
|
|
46
|
+
end
|
|
47
|
+
end
|
|
48
|
+
end
|
|
49
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+
end
|
|
@@ -0,0 +1,86 @@
|
|
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1
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+
require File.join(File.dirname(__FILE__), '../../spec_helper.rb')
|
|
2
|
+
require 'ms/fasta/entry'
|
|
3
|
+
|
|
4
|
+
class FastaEntryTest
|
|
5
|
+
include Ms::Fasta
|
|
6
|
+
|
|
7
|
+
describe 'basic Entry operations' do
|
|
8
|
+
# Abbreviated FASTA entry from wikipedia (http://en.wikipedia.org/wiki/FASTA_format)
|
|
9
|
+
FASTA_0 = %Q{>gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus]
|
|
10
|
+
LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV
|
|
11
|
+
GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX
|
|
12
|
+
IENY
|
|
13
|
+
}
|
|
14
|
+
|
|
15
|
+
#
|
|
16
|
+
# documentation test
|
|
17
|
+
#
|
|
18
|
+
|
|
19
|
+
it 'parses an entry as per docs' do
|
|
20
|
+
entry = Entry.parse %q{
|
|
21
|
+
>gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus]
|
|
22
|
+
LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV
|
|
23
|
+
EWIWGGFSVDKATLNRFFAFHFILPFTMVALAGVHLTFLHETGSNNPLGLTSDSDKIPFHPYYTIKDFLG
|
|
24
|
+
LLILILLLLLLALLSPDMLGDPDNHMPADPLNTPLHIKPEWYFLFAYAILRSVPNKLGGVLALFLSIVIL
|
|
25
|
+
GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX
|
|
26
|
+
IENY
|
|
27
|
+
}.strip
|
|
28
|
+
|
|
29
|
+
entry.header[0,30].is 'gi|5524211|gb|AAD44166.1| cyto'
|
|
30
|
+
entry.sequence[0,30].is 'LCLYTHIGRNIYYGSYLYSETWNTGIMLLL'
|
|
31
|
+
end
|
|
32
|
+
|
|
33
|
+
#
|
|
34
|
+
# class parse tests
|
|
35
|
+
#
|
|
36
|
+
|
|
37
|
+
it 'parses header and sequence' do
|
|
38
|
+
e = Entry.parse(FASTA_0)
|
|
39
|
+
e.header.is "gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus]"
|
|
40
|
+
e.sequence.is(
|
|
41
|
+
"LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV" +
|
|
42
|
+
"GLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX" + "IENY")
|
|
43
|
+
end
|
|
44
|
+
|
|
45
|
+
it 'raises error for entries that do not start with gt' do
|
|
46
|
+
|
|
47
|
+
lambda { Entry.parse "\n#{FASTA_0}" }.should.raise(RuntimeError).message.should.equal("input should begin with '>'")
|
|
48
|
+
end
|
|
49
|
+
|
|
50
|
+
#
|
|
51
|
+
# initialize tests
|
|
52
|
+
#
|
|
53
|
+
|
|
54
|
+
def test_entry_initialization
|
|
55
|
+
e = Entry.new
|
|
56
|
+
assert_equal("", e.header)
|
|
57
|
+
assert_equal("", e.sequence)
|
|
58
|
+
|
|
59
|
+
e = Entry.new "head", "SEQ"
|
|
60
|
+
assert_equal("head", e.header)
|
|
61
|
+
assert_equal("SEQ", e.sequence)
|
|
62
|
+
end
|
|
63
|
+
|
|
64
|
+
#
|
|
65
|
+
# dump tests
|
|
66
|
+
#
|
|
67
|
+
|
|
68
|
+
def test_dump_formats_a_fasta_entry
|
|
69
|
+
e = Entry.new
|
|
70
|
+
assert_equal(">\n", e.dump)
|
|
71
|
+
|
|
72
|
+
e = Entry.new "head", "SEQ"
|
|
73
|
+
assert_equal(">head\nSEQ\n", e.dump)
|
|
74
|
+
end
|
|
75
|
+
|
|
76
|
+
def test_dump_formats_output_with_desired_line_length
|
|
77
|
+
e = Entry.new "header", "ABCDEFGH"
|
|
78
|
+
assert_equal(">header\nABC\nDEF\nGH\n", e.dump("", :line_length => 3))
|
|
79
|
+
end
|
|
80
|
+
|
|
81
|
+
def test_dump_line_length_less_than_1_raises_error
|
|
82
|
+
e = Entry.new
|
|
83
|
+
assert_raise(ArgumentError) { e.dump("", :line_length => 0) }
|
|
84
|
+
end
|
|
85
|
+
end
|
|
86
|
+
end
|
|
@@ -0,0 +1,34 @@
|
|
|
1
|
+
require File.dirname(__FILE__) + '/../../spec_helper'
|
|
2
|
+
|
|
3
|
+
require 'ms/fasta/ipi'
|
|
4
|
+
|
|
5
|
+
class IpiSpec
|
|
6
|
+
include Ms::Fasta
|
|
7
|
+
|
|
8
|
+
describe 'basic IPI operations' do
|
|
9
|
+
|
|
10
|
+
before do
|
|
11
|
+
@headers = ['IPI:IPI00000001.2|SWISS-PROT:O95793-1|TREMBL:A8K622;Q59F99|ENSEMBL:ENSP00000360922;ENSP00000379466|REFSEQ:NP_059347|H-INV:HIT000329496|VEGA:OTTHUMP00000031233 Tax_Id=9606 Gene_Symbol=STAU1 Isoform Long of Double-stranded RNA-binding protein Staufen homolog 1',
|
|
12
|
+
'IPI:IPI00000005.1|SWISS-PROT:P01111|TREMBL:Q5U091|ENSEMBL:ENSP00000358548;ENSP00000385392|REFSEQ:NP_002515|VEGA:OTTHUMP00000013879 Tax_Id=9606 Gene_Symbol=NRAS GTPase NRas']
|
|
13
|
+
|
|
14
|
+
@answers = [{"Gene_Symbol"=>"STAU1", "VEGA"=>"OTTHUMP00000031233", "IPI"=>"IPI00000001.2", "H-INV"=>"HIT000329496", "REFSEQ"=>"NP_059347", "Tax_Id"=>"9606", "SWISS-PROT"=>"O95793-1", "ENSEMBL"=>"ENSP00000360922;ENSP00000379466", "TREMBL"=>"A8K622;Q59F99", "description"=>"Isoform Long of Double-stranded RNA-binding protein Staufen homolog 1"},
|
|
15
|
+
{"Gene_Symbol"=>"NRAS", "VEGA"=>"OTTHUMP00000013879", "IPI"=>"IPI00000005.1", "REFSEQ"=>"NP_002515", "Tax_Id"=>"9606", "SWISS-PROT"=>"P01111", "ENSEMBL"=>"ENSP00000358548;ENSP00000385392", "TREMBL"=>"Q5U091", "description"=>"GTPase NRas"}]
|
|
16
|
+
end
|
|
17
|
+
|
|
18
|
+
it 'parses IPI headers' do
|
|
19
|
+
# assumes that the leading '>' has been removed
|
|
20
|
+
@headers.zip(@answers) do |header, answ|
|
|
21
|
+
Ipi.parse(header).is answ
|
|
22
|
+
end
|
|
23
|
+
end
|
|
24
|
+
|
|
25
|
+
it 'can retrive the IPI ID' do
|
|
26
|
+
answers = ["IPI00000001.2", "IPI00000005.1"]
|
|
27
|
+
|
|
28
|
+
@headers.zip(answers) do |header, answ|
|
|
29
|
+
Ipi.ipi(header).is answ
|
|
30
|
+
end
|
|
31
|
+
end
|
|
32
|
+
|
|
33
|
+
end
|
|
34
|
+
end
|
|
@@ -0,0 +1,76 @@
|
|
|
1
|
+
require File.dirname(__FILE__) + '/../spec_helper'
|
|
2
|
+
|
|
3
|
+
require 'ms/fasta'
|
|
4
|
+
|
|
5
|
+
describe 'basic fasta operations' do
|
|
6
|
+
|
|
7
|
+
before do
|
|
8
|
+
@headers = [">gi|5524211 [hello]", ">another B", ">again C"]
|
|
9
|
+
@entries = ["LCLYTHIGRNIYYGSYLYSETWNTGIMLLLITMATAFMGYVLPWGQMSFWGATVITNLFSAIPYIGTNLV\nGLMPFLHTSKHRSMMLRPLSQALFWTLTMDLLTLTWIGSQPVEYPYTIIGQMASILYFSIILAFLPIAGX\nIENY", "ABCDEF\nGHIJK", "ABCD"]
|
|
10
|
+
@sequences = @entries.map {|v| v.gsub("\n", '') }
|
|
11
|
+
@data = {}
|
|
12
|
+
@data['newlines'] = @headers.zip(@entries).map do |header, data|
|
|
13
|
+
header + "\n" + data
|
|
14
|
+
end.join("\n")
|
|
15
|
+
@data['carriage_returns_and_newlines'] = @data['newlines'].gsub("\n", "\r\n")
|
|
16
|
+
@data.each do |k,v|
|
|
17
|
+
file_key = k + '_file'
|
|
18
|
+
filename = k + '.tmp'
|
|
19
|
+
@data[file_key] = filename
|
|
20
|
+
File.open(filename, 'w') {|out| out.print v }
|
|
21
|
+
end
|
|
22
|
+
end
|
|
23
|
+
|
|
24
|
+
after do
|
|
25
|
+
@data.select {|k,v| k =~ /_file$/ }.each do |k,filename|
|
|
26
|
+
index = filename.sub('.tmp', '.index')
|
|
27
|
+
[filename, index].each do |fn|
|
|
28
|
+
File.unlink(fn) if File.exist? fn
|
|
29
|
+
end
|
|
30
|
+
end
|
|
31
|
+
end
|
|
32
|
+
|
|
33
|
+
def fasta_correct?(fasta)
|
|
34
|
+
fasta.size.is 3
|
|
35
|
+
(0...@headers.size).each do |i|
|
|
36
|
+
header, sequence, entry = @headers[i], @sequences[i], fasta[i]
|
|
37
|
+
entry.header.isnt nil
|
|
38
|
+
entry.sequence.isnt nil
|
|
39
|
+
entry.header.is header[1..-1]
|
|
40
|
+
entry.sequence.is sequence
|
|
41
|
+
end
|
|
42
|
+
end
|
|
43
|
+
|
|
44
|
+
it 'can read a file' do
|
|
45
|
+
%w(newlines_file carriage_returns_and_newlines_file).each do |file|
|
|
46
|
+
Ms::Fasta.open(@data[file]) do |fasta|
|
|
47
|
+
fasta_correct? fasta
|
|
48
|
+
end
|
|
49
|
+
end
|
|
50
|
+
end
|
|
51
|
+
|
|
52
|
+
it 'can read an IO object' do
|
|
53
|
+
%w(newlines_file carriage_returns_and_newlines_file).each do |file|
|
|
54
|
+
File.open(@data[file]) do |io|
|
|
55
|
+
fasta = Ms::Fasta.new(io)
|
|
56
|
+
fasta_correct? fasta
|
|
57
|
+
end
|
|
58
|
+
end
|
|
59
|
+
end
|
|
60
|
+
|
|
61
|
+
it 'can read a string' do
|
|
62
|
+
%w(newlines carriage_returns_and_newlines).each do |key|
|
|
63
|
+
fasta = Ms::Fasta.new @data[key]
|
|
64
|
+
fasta_correct? fasta
|
|
65
|
+
end
|
|
66
|
+
end
|
|
67
|
+
|
|
68
|
+
it 'iterates entries with foreach' do
|
|
69
|
+
%w(newlines_file carriage_returns_and_newlines_file).each do |file|
|
|
70
|
+
Ms::Fasta.foreach(@data[file]) do |entry|
|
|
71
|
+
entry.isa Ms::Fasta::Entry
|
|
72
|
+
end
|
|
73
|
+
end
|
|
74
|
+
end
|
|
75
|
+
|
|
76
|
+
end
|
data/spec/spec_helper.rb
ADDED
metadata
CHANGED
|
@@ -1,78 +1,65 @@
|
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
|
2
2
|
name: ms-fasta
|
|
3
3
|
version: !ruby/object:Gem::Version
|
|
4
|
-
version: 0.
|
|
4
|
+
version: 0.4.0
|
|
5
5
|
platform: ruby
|
|
6
6
|
authors:
|
|
7
|
-
-
|
|
7
|
+
- John T. Prince
|
|
8
8
|
autorequire:
|
|
9
9
|
bindir: bin
|
|
10
10
|
cert_chain: []
|
|
11
11
|
|
|
12
|
-
date: 2009-
|
|
12
|
+
date: 2009-12-09 00:00:00 -07:00
|
|
13
13
|
default_executable:
|
|
14
14
|
dependencies:
|
|
15
15
|
- !ruby/object:Gem::Dependency
|
|
16
|
-
name:
|
|
17
|
-
type: :runtime
|
|
18
|
-
version_requirement:
|
|
19
|
-
version_requirements: !ruby/object:Gem::Requirement
|
|
20
|
-
requirements:
|
|
21
|
-
- - ">="
|
|
22
|
-
- !ruby/object:Gem::Version
|
|
23
|
-
version: 0.17.1
|
|
24
|
-
version:
|
|
25
|
-
- !ruby/object:Gem::Dependency
|
|
26
|
-
name: tap-test
|
|
16
|
+
name: spec-more
|
|
27
17
|
type: :development
|
|
28
18
|
version_requirement:
|
|
29
19
|
version_requirements: !ruby/object:Gem::Requirement
|
|
30
20
|
requirements:
|
|
31
21
|
- - ">="
|
|
32
22
|
- !ruby/object:Gem::Version
|
|
33
|
-
version:
|
|
34
|
-
version:
|
|
35
|
-
- !ruby/object:Gem::Dependency
|
|
36
|
-
name: external
|
|
37
|
-
type: :runtime
|
|
38
|
-
version_requirement:
|
|
39
|
-
version_requirements: !ruby/object:Gem::Requirement
|
|
40
|
-
requirements:
|
|
41
|
-
- - ">="
|
|
42
|
-
- !ruby/object:Gem::Version
|
|
43
|
-
version: 0.3.0
|
|
23
|
+
version: 1.1.0
|
|
44
24
|
version:
|
|
45
|
-
description:
|
|
46
|
-
email:
|
|
25
|
+
description: provides programmatic access to fasta files
|
|
26
|
+
email: jtprince@gmail.com
|
|
47
27
|
executables: []
|
|
48
28
|
|
|
49
29
|
extensions: []
|
|
50
30
|
|
|
51
31
|
extra_rdoc_files:
|
|
52
|
-
-
|
|
32
|
+
- LICENSE
|
|
53
33
|
- README.rdoc
|
|
54
|
-
- MIT-LICENSE
|
|
55
34
|
files:
|
|
35
|
+
- .gitignore
|
|
36
|
+
- History
|
|
37
|
+
- LICENSE
|
|
38
|
+
- README.rdoc
|
|
39
|
+
- Rakefile
|
|
40
|
+
- VERSION
|
|
56
41
|
- lib/ms/fasta.rb
|
|
57
42
|
- lib/ms/fasta/archive.rb
|
|
58
43
|
- lib/ms/fasta/entry.rb
|
|
44
|
+
- lib/ms/fasta/ipi.rb
|
|
45
|
+
- lib/ms/fasta/ipi/dat.rb
|
|
59
46
|
- lib/ms/load/fasta.rb
|
|
60
47
|
- lib/ms/random/fasta.rb
|
|
61
48
|
- lib/ms/select/fasta.rb
|
|
49
|
+
- spec/ms/fasta/archive_spec.rb
|
|
50
|
+
- spec/ms/fasta/entry_spec.rb
|
|
51
|
+
- spec/ms/fasta/ipi/dat_spec.rb
|
|
52
|
+
- spec/ms/fasta/ipi_spec.rb
|
|
53
|
+
- spec/ms/fasta_spec.rb
|
|
54
|
+
- spec/spec_helper.rb
|
|
62
55
|
- tap.yml
|
|
63
|
-
- History
|
|
64
|
-
- README.rdoc
|
|
65
|
-
- MIT-LICENSE
|
|
66
56
|
has_rdoc: true
|
|
67
|
-
homepage: http://
|
|
57
|
+
homepage: http://jtprince.github.com/ms-fasta
|
|
58
|
+
licenses: []
|
|
59
|
+
|
|
68
60
|
post_install_message:
|
|
69
61
|
rdoc_options:
|
|
70
|
-
- --
|
|
71
|
-
- README.rdoc
|
|
72
|
-
- -S
|
|
73
|
-
- -N
|
|
74
|
-
- --title
|
|
75
|
-
- Ms-Fasta
|
|
62
|
+
- --charset=UTF-8
|
|
76
63
|
require_paths:
|
|
77
64
|
- lib
|
|
78
65
|
required_ruby_version: !ruby/object:Gem::Requirement
|
|
@@ -90,9 +77,14 @@ required_rubygems_version: !ruby/object:Gem::Requirement
|
|
|
90
77
|
requirements: []
|
|
91
78
|
|
|
92
79
|
rubyforge_project: mspire
|
|
93
|
-
rubygems_version: 1.3.
|
|
80
|
+
rubygems_version: 1.3.5
|
|
94
81
|
signing_key:
|
|
95
|
-
specification_version:
|
|
96
|
-
summary:
|
|
97
|
-
test_files:
|
|
98
|
-
|
|
82
|
+
specification_version: 3
|
|
83
|
+
summary: An mspire library for working with fasta formatted files
|
|
84
|
+
test_files:
|
|
85
|
+
- spec/ms/fasta/archive_spec.rb
|
|
86
|
+
- spec/ms/fasta/ipi_spec.rb
|
|
87
|
+
- spec/ms/fasta/ipi/dat_spec.rb
|
|
88
|
+
- spec/ms/fasta/entry_spec.rb
|
|
89
|
+
- spec/ms/fasta_spec.rb
|
|
90
|
+
- spec/spec_helper.rb
|