genfrag 0.0.0.1

Sign up to get free protection for your applications and to get access to all the features.
Files changed (47) hide show
  1. data/.bnsignore +16 -0
  2. data/History.txt +4 -0
  3. data/LICENSE.txt +58 -0
  4. data/README.rdoc +40 -0
  5. data/Rakefile +53 -0
  6. data/bin/genfrag +8 -0
  7. data/lib/genfrag.rb +129 -0
  8. data/lib/genfrag/app.rb +105 -0
  9. data/lib/genfrag/app/command.rb +145 -0
  10. data/lib/genfrag/app/index_command.rb +227 -0
  11. data/lib/genfrag/app/index_command/db.rb +105 -0
  12. data/lib/genfrag/app/search_command.rb +298 -0
  13. data/lib/genfrag/app/search_command/match.rb +165 -0
  14. data/lib/genfrag/app/search_command/process_file.rb +125 -0
  15. data/lib/genfrag/app/search_command/trim.rb +121 -0
  16. data/lib/genfrag/debug.rb +0 -0
  17. data/spec/data/index_command/in/a.fasta +109 -0
  18. data/spec/data/index_command/out/1-a_lookup.tdf +4 -0
  19. data/spec/data/index_command/out/2-a_lookup.db +0 -0
  20. data/spec/data/index_command/out/3-a_lookup.tdf +2 -0
  21. data/spec/data/index_command/out/4-a_lookup.db +0 -0
  22. data/spec/data/index_command/out/5-a_lookup.tdf +4 -0
  23. data/spec/data/index_command/out/6-a_lookup.db +0 -0
  24. data/spec/data/index_command/out/a.fasta.db +0 -0
  25. data/spec/data/index_command/out/a.fasta.tdf +6 -0
  26. data/spec/genfrag/app/command_spec.rb +55 -0
  27. data/spec/genfrag/app/index_command_spec.rb +258 -0
  28. data/spec/genfrag/app/search_command/match_spec.rb +77 -0
  29. data/spec/genfrag/app/search_command/process_file_spec.rb +185 -0
  30. data/spec/genfrag/app/search_command/trim_spec.rb +75 -0
  31. data/spec/genfrag/app/search_command_spec.rb +260 -0
  32. data/spec/genfrag/app_spec.rb +77 -0
  33. data/spec/genfrag_spec.rb +87 -0
  34. data/spec/spec_helper.rb +56 -0
  35. data/tasks/ann.rake +80 -0
  36. data/tasks/bones.rake +20 -0
  37. data/tasks/gem.rake +201 -0
  38. data/tasks/git.rake +40 -0
  39. data/tasks/notes.rake +27 -0
  40. data/tasks/post_load.rake +34 -0
  41. data/tasks/rdoc.rake +50 -0
  42. data/tasks/rubyforge.rake +55 -0
  43. data/tasks/setup.rb +300 -0
  44. data/tasks/spec.rake +54 -0
  45. data/tasks/svn.rake +47 -0
  46. data/tasks/test.rake +40 -0
  47. metadata +136 -0
@@ -0,0 +1,56 @@
1
+ # Equivalent to a header guard in C/C++
2
+ # Used to prevent the spec helper from being loaded more than once
3
+ unless defined? GENFRAG_SPEC_HELPER
4
+ GENFRAG_SPEC_HELPER = true
5
+
6
+ require 'stringio'
7
+ require 'tmpdir'
8
+ require File.expand_path(
9
+ File.join(File.dirname(__FILE__), %w[.. lib genfrag]))
10
+
11
+ GENFRAG_SPEC_DATA_DIR = File.join(File.dirname(__FILE__), %w[data])
12
+
13
+ GENFRAG_SPEC_TMP_DIR = File.join(Dir.tmpdir, %w[genfrag])
14
+ puts "tmp dir is #{GENFRAG_SPEC_TMP_DIR}"
15
+
16
+ def compare(filename, ext)
17
+ generated = File.join(@working_output_dir, filename + ext)
18
+ frozen = File.join(@frozen_output_dir, filename + ext)
19
+ FileUtils.compare_file(generated, frozen)
20
+ end
21
+
22
+ Spec::Runner.configure do |config|
23
+ # == Mock Framework
24
+ #
25
+ # RSpec uses it's own mocking framework by default. If you prefer to
26
+ # use mocha, flexmock or RR, uncomment the appropriate line:
27
+ #
28
+ # config.mock_with :mocha
29
+ # config.mock_with :flexmock
30
+ # config.mock_with :rr
31
+ end
32
+
33
+ class StringIO
34
+ alias :_readline :readline
35
+ def readline
36
+ @_pos ||= 0
37
+ seek @_pos
38
+ begin
39
+ _line = _readline
40
+ @_pos = tell
41
+ _line.rstrip
42
+ rescue EOFError
43
+ nil
44
+ end
45
+ end
46
+
47
+ def clear
48
+ truncate 0
49
+ seek 0
50
+ @_pos = 0
51
+ end
52
+ end
53
+
54
+ end # unless defined?
55
+
56
+ # EOF
@@ -0,0 +1,80 @@
1
+
2
+ begin
3
+ require 'bones/smtp_tls'
4
+ rescue LoadError
5
+ require 'net/smtp'
6
+ end
7
+ require 'time'
8
+
9
+ namespace :ann do
10
+
11
+ # A prerequisites task that all other tasks depend upon
12
+ task :prereqs
13
+
14
+ file PROJ.ann.file do
15
+ ann = PROJ.ann
16
+ puts "Generating #{ann.file}"
17
+ File.open(ann.file,'w') do |fd|
18
+ fd.puts("#{PROJ.name} version #{PROJ.version}")
19
+ fd.puts(" by #{Array(PROJ.authors).first}") if PROJ.authors
20
+ fd.puts(" #{PROJ.url}") if PROJ.url.valid?
21
+ fd.puts(" (the \"#{PROJ.release_name}\" release)") if PROJ.release_name
22
+ fd.puts
23
+ fd.puts("== DESCRIPTION")
24
+ fd.puts
25
+ fd.puts(PROJ.description)
26
+ fd.puts
27
+ fd.puts(PROJ.changes.sub(%r/^.*$/, '== CHANGES'))
28
+ fd.puts
29
+ ann.paragraphs.each do |p|
30
+ fd.puts "== #{p.upcase}"
31
+ fd.puts
32
+ fd.puts paragraphs_of(PROJ.readme_file, p).join("\n\n")
33
+ fd.puts
34
+ end
35
+ fd.puts ann.text if ann.text
36
+ end
37
+ end
38
+
39
+ desc "Create an announcement file"
40
+ task :announcement => ['ann:prereqs', PROJ.ann.file]
41
+
42
+ desc "Send an email announcement"
43
+ task :email => ['ann:prereqs', PROJ.ann.file] do
44
+ ann = PROJ.ann
45
+ from = ann.email[:from] || Array(PROJ.authors).first || PROJ.email
46
+ to = Array(ann.email[:to])
47
+
48
+ ### build a mail header for RFC 822
49
+ rfc822msg = "From: #{from}\n"
50
+ rfc822msg << "To: #{to.join(',')}\n"
51
+ rfc822msg << "Subject: [ANN] #{PROJ.name} #{PROJ.version}"
52
+ rfc822msg << " (#{PROJ.release_name})" if PROJ.release_name
53
+ rfc822msg << "\n"
54
+ rfc822msg << "Date: #{Time.new.rfc822}\n"
55
+ rfc822msg << "Message-Id: "
56
+ rfc822msg << "<#{"%.8f" % Time.now.to_f}@#{ann.email[:domain]}>\n\n"
57
+ rfc822msg << File.read(ann.file)
58
+
59
+ params = [:server, :port, :domain, :acct, :passwd, :authtype].map do |key|
60
+ ann.email[key]
61
+ end
62
+
63
+ params[3] = PROJ.email if params[3].nil?
64
+
65
+ if params[4].nil?
66
+ STDOUT.write "Please enter your e-mail password (#{params[3]}): "
67
+ params[4] = STDIN.gets.chomp
68
+ end
69
+
70
+ ### send email
71
+ Net::SMTP.start(*params) {|smtp| smtp.sendmail(rfc822msg, from, to)}
72
+ end
73
+ end # namespace :ann
74
+
75
+ desc 'Alias to ann:announcement'
76
+ task :ann => 'ann:announcement'
77
+
78
+ CLOBBER << PROJ.ann.file
79
+
80
+ # EOF
@@ -0,0 +1,20 @@
1
+
2
+ if HAVE_BONES
3
+
4
+ namespace :bones do
5
+
6
+ desc 'Show the PROJ open struct'
7
+ task :debug do |t|
8
+ atr = if t.application.top_level_tasks.length == 2
9
+ t.application.top_level_tasks.pop
10
+ end
11
+
12
+ if atr then Bones::Debug.show_attr(PROJ, atr)
13
+ else Bones::Debug.show PROJ end
14
+ end
15
+
16
+ end # namespace :bones
17
+
18
+ end # HAVE_BONES
19
+
20
+ # EOF
@@ -0,0 +1,201 @@
1
+
2
+ require 'find'
3
+ require 'rake/packagetask'
4
+ require 'rubygems/user_interaction'
5
+ require 'rubygems/builder'
6
+
7
+ module Bones
8
+ class GemPackageTask < Rake::PackageTask
9
+ # Ruby GEM spec containing the metadata for this package. The
10
+ # name, version and package_files are automatically determined
11
+ # from the GEM spec and don't need to be explicitly provided.
12
+ #
13
+ attr_accessor :gem_spec
14
+
15
+ # Tasks from the Bones gem directory
16
+ attr_reader :bones_files
17
+
18
+ # Create a GEM Package task library. Automatically define the gem
19
+ # if a block is given. If no block is supplied, then +define+
20
+ # needs to be called to define the task.
21
+ #
22
+ def initialize(gem_spec)
23
+ init(gem_spec)
24
+ yield self if block_given?
25
+ define if block_given?
26
+ end
27
+
28
+ # Initialization tasks without the "yield self" or define
29
+ # operations.
30
+ #
31
+ def init(gem)
32
+ super(gem.name, gem.version)
33
+ @gem_spec = gem
34
+ @package_files += gem_spec.files if gem_spec.files
35
+ @bones_files = []
36
+
37
+ local_setup = File.join(Dir.pwd, %w[tasks setup.rb])
38
+ if !test(?e, local_setup)
39
+ Dir.glob(::Bones.path(%w[lib bones tasks *])).each {|fn| bones_files << fn}
40
+ end
41
+ end
42
+
43
+ # Create the Rake tasks and actions specified by this
44
+ # GemPackageTask. (+define+ is automatically called if a block is
45
+ # given to +new+).
46
+ #
47
+ def define
48
+ super
49
+ task :prereqs
50
+ task :package => ['gem:prereqs', "#{package_dir_path}/#{gem_file}"]
51
+ file "#{package_dir_path}/#{gem_file}" => [package_dir_path] + package_files + bones_files do
52
+ when_writing("Creating GEM") {
53
+ chdir(package_dir_path) do
54
+ Gem::Builder.new(gem_spec).build
55
+ verbose(true) {
56
+ mv gem_file, "../#{gem_file}"
57
+ }
58
+ end
59
+ }
60
+ end
61
+
62
+ file package_dir_path => bones_files do
63
+ mkdir_p package_dir rescue nil
64
+
65
+ gem_spec.files = (gem_spec.files +
66
+ bones_files.map {|fn| File.join('tasks', File.basename(fn))}).sort
67
+
68
+ bones_files.each do |fn|
69
+ base_fn = File.join('tasks', File.basename(fn))
70
+ f = File.join(package_dir_path, base_fn)
71
+ fdir = File.dirname(f)
72
+ mkdir_p(fdir) if !File.exist?(fdir)
73
+ if File.directory?(fn)
74
+ mkdir_p(f)
75
+ else
76
+ raise "file name conflict for '#{base_fn}' (conflicts with '#{fn}')" if test(?e, f)
77
+ safe_ln(fn, f)
78
+ end
79
+ end
80
+ end
81
+ end
82
+
83
+ def gem_file
84
+ if @gem_spec.platform == Gem::Platform::RUBY
85
+ "#{package_name}.gem"
86
+ else
87
+ "#{package_name}-#{@gem_spec.platform}.gem"
88
+ end
89
+ end
90
+ end # class GemPackageTask
91
+ end # module Bones
92
+
93
+ namespace :gem do
94
+
95
+ PROJ.gem._spec = Gem::Specification.new do |s|
96
+ s.name = PROJ.name
97
+ s.version = PROJ.version
98
+ s.summary = PROJ.summary
99
+ s.authors = Array(PROJ.authors)
100
+ s.email = PROJ.email
101
+ s.homepage = Array(PROJ.url).first
102
+ s.rubyforge_project = PROJ.rubyforge.name
103
+
104
+ s.description = PROJ.description
105
+
106
+ PROJ.gem.dependencies.each do |dep|
107
+ s.add_dependency(*dep)
108
+ end
109
+
110
+ PROJ.gem.development_dependencies.each do |dep|
111
+ s.add_development_dependency(*dep)
112
+ end
113
+
114
+ s.files = PROJ.gem.files
115
+ s.executables = PROJ.gem.executables.map {|fn| File.basename(fn)}
116
+ s.extensions = PROJ.gem.files.grep %r/extconf\.rb$/
117
+
118
+ s.bindir = 'bin'
119
+ dirs = Dir["{#{PROJ.libs.join(',')}}"]
120
+ s.require_paths = dirs unless dirs.empty?
121
+
122
+ incl = Regexp.new(PROJ.rdoc.include.join('|'))
123
+ excl = PROJ.rdoc.exclude.dup.concat %w[\.rb$ ^(\.\/|\/)?ext]
124
+ excl = Regexp.new(excl.join('|'))
125
+ rdoc_files = PROJ.gem.files.find_all do |fn|
126
+ case fn
127
+ when excl; false
128
+ when incl; true
129
+ else false end
130
+ end
131
+ s.rdoc_options = PROJ.rdoc.opts + ['--main', PROJ.rdoc.main]
132
+ s.extra_rdoc_files = rdoc_files
133
+ s.has_rdoc = true
134
+
135
+ if test ?f, PROJ.test.file
136
+ s.test_file = PROJ.test.file
137
+ else
138
+ s.test_files = PROJ.test.files.to_a
139
+ end
140
+
141
+ # Do any extra stuff the user wants
142
+ PROJ.gem.extras.each do |msg, val|
143
+ case val
144
+ when Proc
145
+ val.call(s.send(msg))
146
+ else
147
+ s.send "#{msg}=", val
148
+ end
149
+ end
150
+ end # Gem::Specification.new
151
+
152
+ Bones::GemPackageTask.new(PROJ.gem._spec) do |pkg|
153
+ pkg.need_tar = PROJ.gem.need_tar
154
+ pkg.need_zip = PROJ.gem.need_zip
155
+ end
156
+
157
+ desc 'Show information about the gem'
158
+ task :debug => 'gem:prereqs' do
159
+ puts PROJ.gem._spec.to_ruby
160
+ end
161
+
162
+ desc 'Write the gemspec '
163
+ task :spec => 'gem:prereqs' do
164
+ File.open("#{PROJ.name}.gemspec", 'w') do |f|
165
+ f.write PROJ.gem._spec.to_ruby
166
+ end
167
+ end
168
+
169
+ desc 'Install the gem'
170
+ task :install => [:clobber, 'gem:package'] do
171
+ sh "#{SUDO} #{GEM} install --local pkg/#{PROJ.gem._spec.full_name}"
172
+
173
+ # use this version of the command for rubygems > 1.0.0
174
+ #sh "#{SUDO} #{GEM} install --no-update-sources pkg/#{PROJ.gem._spec.full_name}"
175
+ end
176
+
177
+ desc 'Uninstall the gem'
178
+ task :uninstall do
179
+ installed_list = Gem.source_index.find_name(PROJ.name)
180
+ if installed_list and installed_list.collect { |s| s.version.to_s}.include?(PROJ.version) then
181
+ sh "#{SUDO} #{GEM} uninstall --version '#{PROJ.version}' --ignore-dependencies --executables #{PROJ.name}"
182
+ end
183
+ end
184
+
185
+ desc 'Reinstall the gem'
186
+ task :reinstall => [:uninstall, :install]
187
+
188
+ desc 'Cleanup the gem'
189
+ task :cleanup do
190
+ sh "#{SUDO} #{GEM} cleanup #{PROJ.gem._spec.name}"
191
+ end
192
+ end # namespace :gem
193
+
194
+
195
+ desc 'Alias to gem:package'
196
+ task :gem => 'gem:package'
197
+
198
+ task :clobber => 'gem:clobber_package'
199
+ remove_desc_for_task 'gem:clobber_package'
200
+
201
+ # EOF
@@ -0,0 +1,40 @@
1
+
2
+ if HAVE_GIT
3
+
4
+ namespace :git do
5
+
6
+ # A prerequisites task that all other tasks depend upon
7
+ task :prereqs
8
+
9
+ desc 'Show tags from the Git repository'
10
+ task :show_tags => 'git:prereqs' do |t|
11
+ puts %x/git tag/
12
+ end
13
+
14
+ desc 'Create a new tag in the Git repository'
15
+ task :create_tag => 'git:prereqs' do |t|
16
+ v = ENV['VERSION'] or abort 'Must supply VERSION=x.y.z'
17
+ abort "Versions don't match #{v} vs #{PROJ.version}" if v != PROJ.version
18
+
19
+ tag = "%s-%s" % [PROJ.name, PROJ.version]
20
+ msg = "Creating tag for #{PROJ.name} version #{PROJ.version}"
21
+
22
+ puts "Creating Git tag '#{tag}'"
23
+ unless system "git tag -a -m '#{msg}' #{tag}"
24
+ abort "Tag creation failed"
25
+ end
26
+
27
+ if %x/git remote/ =~ %r/^origin\s*$/
28
+ unless system "git push origin #{tag}"
29
+ abort "Could not push tag to remote Git repository"
30
+ end
31
+ end
32
+ end
33
+
34
+ end # namespace :git
35
+
36
+ task 'gem:release' => 'git:create_tag'
37
+
38
+ end # if HAVE_GIT
39
+
40
+ # EOF
@@ -0,0 +1,27 @@
1
+
2
+ if HAVE_BONES
3
+
4
+ desc "Enumerate all annotations"
5
+ task :notes do |t|
6
+ id = if t.application.top_level_tasks.length > 1
7
+ t.application.top_level_tasks.slice!(1..-1).join(' ')
8
+ end
9
+ Bones::AnnotationExtractor.enumerate(
10
+ PROJ, PROJ.notes.tags.join('|'), id, :tag => true)
11
+ end
12
+
13
+ namespace :notes do
14
+ PROJ.notes.tags.each do |tag|
15
+ desc "Enumerate all #{tag} annotations"
16
+ task tag.downcase.to_sym do |t|
17
+ id = if t.application.top_level_tasks.length > 1
18
+ t.application.top_level_tasks.slice!(1..-1).join(' ')
19
+ end
20
+ Bones::AnnotationExtractor.enumerate(PROJ, tag, id)
21
+ end
22
+ end
23
+ end
24
+
25
+ end # if HAVE_BONES
26
+
27
+ # EOF
@@ -0,0 +1,34 @@
1
+
2
+ # This file does not define any rake tasks. It is used to load some project
3
+ # settings if they are not defined by the user.
4
+
5
+ PROJ.exclude << ["^#{Regexp.escape(PROJ.ann.file)}$",
6
+ "^#{Regexp.escape(PROJ.ignore_file)}$",
7
+ "^#{Regexp.escape(PROJ.rdoc.dir)}/",
8
+ "^#{Regexp.escape(PROJ.rcov.dir)}/"]
9
+
10
+ flatten_arrays = lambda do |this,os|
11
+ os.instance_variable_get(:@table).each do |key,val|
12
+ next if key == :dependencies \
13
+ or key == :development_dependencies
14
+ case val
15
+ when Array; val.flatten!
16
+ when OpenStruct; this.call(this,val)
17
+ end
18
+ end
19
+ end
20
+ flatten_arrays.call(flatten_arrays,PROJ)
21
+
22
+ PROJ.changes ||= paragraphs_of(PROJ.history_file, 0..1).join("\n\n")
23
+
24
+ PROJ.description ||= paragraphs_of(PROJ.readme_file, 'description').join("\n\n")
25
+
26
+ PROJ.summary ||= PROJ.description.split('.').first
27
+
28
+ PROJ.gem.files ||= manifest
29
+
30
+ PROJ.gem.executables ||= PROJ.gem.files.find_all {|fn| fn =~ %r/^bin/}
31
+
32
+ PROJ.rdoc.main ||= PROJ.readme_file
33
+
34
+ # EOF