bio-maf 0.2.0-java → 0.3.0-java

data/.gitignore

@@ -51,3 +51,4 @@ pkg
 # Ignore Gemfile.lock for gems. See http://yehudakatz.com/2010/12/16/clarifying-the-roles-of-the-gemspec-and-gemfile/
 Gemfile.lock
 
+tmp

data/Gemfile

@@ -13,7 +13,7 @@ group :development do
   gem "redcarpet", "~> 2.1.1", :platforms => :mri
   gem "ronn", "~> 0.7.3", :platforms => :mri
   gem "sinatra", "~> 1.3.2" # for ronn --server
-  gem "rubygems-tasks", "~> 0.2.3"
+  gem "jruby-openssl", ">= 0.7", :platforms => :jruby
 end
 
 group :test do
@@ -21,4 +21,6 @@ group :test do
   gem "rake", ">= 0.9"
   gem "cucumber", ">= 0"
   gem "rspec", "~> 2.10.0"
+  gem "rubygems-tasks", "~> 0.2.3"
+  gem "aruba", "~> 0.4.11"
 end

data/README.md

@@ -92,6 +92,19 @@ Or programmatically:
 
 Refer to [`mm8_chr7_tiny.maf`](https://github.com/csw/bioruby-maf/blob/master/test/data/mm8_chr7_tiny.maf).
 
+    require 'bio-maf'
+    access = Bio::MAF::Access.maf_dir('test/data')
+
+    q = [Bio::GenomicInterval.zero_based('mm8.chr7', 80082592, 80082766)]
+    access.find(q) do |block|
+      ref_seq = block.sequences[0]
+      puts "Matched block at #{ref_seq.start}, #{ref_seq.size} bases"
+    end
+
+    # => Matched block at 80082592, 121 bases
+    # => Matched block at 80082713, 54 bases
+
+Or, equivalently, one can work with a specific MAF file and index directly:
 
     require 'bio-maf'
     parser = Bio::MAF::Parser.new('test/data/mm8_chr7_tiny.maf')
@@ -106,15 +119,27 @@ Refer to [`mm8_chr7_tiny.maf`](https://github.com/csw/bioruby-maf/blob/master/te
     # => Matched block at 80082592, 121 bases
     # => Matched block at 80082713, 54 bases
 
+### Extract alignment blocks truncated to a given interval
+
+Given a genomic interval of interest, one can also extract only the
+subsets of blocks that intersect with that interval, using the
+`#slice` method like so:
+
+    require 'bio-maf'
+    access = Bio::MAF::Access.maf_dir('test/data')
+    int = Bio::GenomicInterval.zero_based('mm8.chr7', 80082350, 80082380)
+    blocks = access.slice(int).to_a
+    puts "Got #{blocks.size} blocks, first #{blocks.first.ref_seq.size} base pairs."
+    # => Got 2 blocks, first 18 base pairs.
+
 ### Filter species returned in alignment blocks
 
     require 'bio-maf'
-    parser = Bio::MAF::Parser.new('test/data/mm8_chr7_tiny.maf')
-    idx = Bio::MAF::KyotoIndex.open('test/data/mm8_chr7_tiny.kct')
+    access = Bio::MAF::Access.maf_dir('test/data')
 
-    parser.sequence_filter = { :only_species => %w(hg18 mm8 rheMac2) }
+    access.sequence_filter = { :only_species => %w(hg18 mm8 rheMac2) }
     q = [Bio::GenomicInterval.zero_based('mm8.chr7', 80082592, 80082766)]
-    blocks = idx.find(q, parser)
+    blocks = access.find(q)
     block = blocks.first
     puts "Block has #{block.sequences.size} sequences."
 
@@ -129,23 +154,26 @@ See also the [Cucumber feature][] and [step definitions][] for this.
 
 #### Match only blocks with all specified species
 
+    access = Bio::MAF::Access.maf_dir('test/data')
     q = [Bio::GenomicInterval.zero_based('mm8.chr7', 80082471, 80082730)]
-    filter = { :with_all_species => %w(panTro2 loxAfr1) }
-    n_blocks = idx.find(q, parser, filter).count
+    access.block_filter = { :with_all_species => %w(panTro2 loxAfr1) }
+    n_blocks = access.find(q).count
     # => 1
 
 #### Match only blocks with a certain number of sequences
 
+    access = Bio::MAF::Access.maf_dir('test/data')
     q = [Bio::GenomicInterval.zero_based('mm8.chr7', 80082767, 80083008)]
-    filter = { :at_least_n_sequences => 6 }
-    n_blocks = idx.find(q, parser, filter).count
+    access.block_filter = { :at_least_n_sequences => 6 }
+    n_blocks = access.find(q).count
     # => 1
 
 #### Match only blocks within a text size range
 
+    access = Bio::MAF::Access.maf_dir('test/data')
     q = [Bio::GenomicInterval.zero_based('mm8.chr7', 0, 80100000)]
-    filter = { :min_size => 72, :max_size => 160 }
-    n_blocks = idx.find(q, parser, filter).count
+    access.block_filter = { :min_size => 72, :max_size => 160 }
+    n_blocks = access.find(q).count
     # => 3
 
 ### Process each block in a MAF file
@@ -155,7 +183,7 @@ See also the [Cucumber feature][] and [step definitions][] for this.
     puts "MAF version: #{p.header.version}"
     # => MAF version: 1
 
-    p.parse_blocks.each do |block|
+    p.each_block do |block|
       block.sequences.each do |seq|
         do_something(seq)
       end
@@ -183,6 +211,12 @@ Refer to [`chr22_ieq.maf`](https://github.com/csw/bioruby-maf/blob/master/test/d
     #      @size=1601, @strand=:+, @src_size=50103, @text=nil,
     #      @status="I"> 
 
+Such options can also be set on a Bio::MAF::Access object:
+
+    require 'bio-maf'
+    access = Bio::MAF::Access.maf_dir('test/data')
+    access.parse_options[:parse_empty] = true
+
 ### Remove gaps from parsed blocks
 
 After filtering out species with
@@ -192,8 +226,42 @@ sequences that were filtered out. Such gaps can be removed by setting
 the `:remove_gaps` parser option:
 
     require 'bio-maf'
-    p = Bio::MAF::Parser.new('test/data/chr22_ieq.maf',
-                             :remove_gaps => true)
+    access = Bio::MAF::Access.maf_dir('test/data')
+    access.parse_options[:remove_gaps] = true
+
+### Join blocks after filtering together
+
+Similarly, filtering out species may remove a species which had caused
+two adjacent alignment blocks to be split. By enabling the
+`:join_blocks` parser option, such blocks can be joined together:
+
+    require 'bio-maf'
+    access = Bio::MAF::Access.maf_dir('test/data')
+    access.parse_options[:join_blocks] = true
+
+See the [Cucumber feature][] for more details.
+
+[Cucumber feature]: https://github.com/csw/bioruby-maf/blob/master/features/block-joining.feature
+
+### Extract bio-alignment representations of blocks
+
+When the `:as_bio_alignment` parser option is given, blocks will be
+returned as [Bio::BioAlignment::Alignment][] objects as used in the
+[bio-alignment] Biogem. This offers a great deal of built-in
+functionality for column-wise operations, alignment manipulation, and
+more.
+
+[Bio::BioAlignment::Alignment]: http://rdoc.info/gems/bio-alignment/Bio/BioAlignment/Alignment
+[bio-alignment]: https://github.com/pjotrp/bioruby-alignment
+
+    require 'bio-maf'
+    access = Bio::MAF::Access.maf_dir('test/data')
+    access.parse_options[:as_bio_alignment] = true
+    q = [Bio::GenomicInterval.zero_based('mm8.chr7', 80082592, 80082766)]
+    access.find(q) do |aln|
+      col = aln.columns[3]
+      puts "bases in column 3: #{col}"
+    end
 
 ### Tile blocks together over an interval
 
@@ -206,24 +274,25 @@ the
 [`maf_tile(1)`](http://csw.github.com/bioruby-maf/man/maf_tile.1.html)
 man page.
 
-[feature]: https://github.com/csw/bioruby-maf/blob/master/features/gap-filling.feature
+[feature]: https://github.com/csw/bioruby-maf/blob/master/features/tiling.feature
 
     require 'bio-maf'
-    tiler = Bio::MAF::Tiler.new
-    tiler.index = Bio::MAF::KyotoIndex.open('test/data/mm8_chr7_tiny.kct')
-    tiler.parser = Bio::MAF::Parser.new('test/data/mm8_chr7_tiny.maf')
-    # optional
-    tiler.reference = Bio::MAF::FASTARangeReader.new('reference.fa.gz')
-    tiler.species = %w(mm8 rn4 hg18)
-    tiler.species_map = {
-      'mm8' => 'mouse',
-      'rn4' => 'rat',
-      'hg18' => 'human'
-    }
-    tiler.interval = Bio::GenomicInterval.zero_based('mm8.chr7',
-                                                     80082334,
-                                                     80082468)
-    tiler.write_fasta($stdout)
+    access = Bio::MAF::Access.maf_dir('test/data')
+    interval = Bio::GenomicInterval.zero_based('mm8.chr7',
+                                               80082334,
+                                               80082468)
+    access.tile(interval) do |tiler|
+      # reference is optional
+      tiler.reference = 'reference.fa.gz'
+      tiler.species = %w(mm8 rn4 hg18)
+      # species_map is optional
+      tiler.species_map = {
+        'mm8' => 'mouse',
+        'rn4' => 'rat',
+        'hg18' => 'human'
+      }
+      tiler.write_fasta($stdout)
+    end
 
 ### Command line tools
 

data/Rakefile

@@ -23,7 +23,10 @@ RSpec::Core::RakeTask.new(:spec) do |spec|
 end
 
 require 'cucumber/rake/task'
-Cucumber::Rake::Task.new do |features|
+Cucumber::Rake::Task.new do |t|
+  opts = "features"
+  opts << ' --tags ~@no_jruby' if RUBY_PLATFORM == 'java'
+  t.cucumber_opts = opts
 end
 
 task :test => [ :spec, :cucumber ] 
@@ -44,7 +47,8 @@ if ronn_avail
   desc "Generate man pages"
   task :man do
     file_spec = RONN_FILES.join(' ')
-    sh "ronn --roff --html --style toc --date #{$gemspec.date.strftime('%Y-%m-%d')} --manual='BioRuby Manual' --organization='#{$gemspec.author}' #{file_spec}"
+    #sh "ronn --roff --html --style toc --date #{$gemspec.date.strftime('%Y-%m-%d')} --manual='BioRuby Manual' --organization='#{$gemspec.author}' #{file_spec}"
+    sh "ronn --roff --html --style toc --date #{Time.now.strftime('%Y-%m-%d')} --manual='BioRuby Manual' --organization='BioRuby' #{file_spec}"
   end
 
   namespace :man do

data/bin/maf_tile

@@ -6,6 +6,24 @@ require 'ostruct'
 require 'bio-maf'
 require 'bio-genomic-interval'
 
+def parse_interval(line)
+  src, r_start_s, r_end_s, _ = line.split(nil, 4)
+  r_start = r_start_s.to_i
+  r_end = r_end_s.to_i
+  return Bio::GenomicInterval.zero_based(src, r_start, r_end)
+end
+
+def target_for(base, interval, &blk)
+  path = "#{base}_#{interval.zero_start}-#{interval.zero_end}.fa"
+  File.open(path, 'w', &blk)
+end
+
+def apply_options(options, tiler)
+  tiler.reference = options.ref if options.ref
+  tiler.species = options.species
+  tiler.species_map = options.species_map
+end
+
 options = OpenStruct.new
 options.p = { :threads => 1 }
 options.species = []
@@ -13,16 +31,20 @@ options.species_map = {}
 options.usage = false
 
 o_parser = OptionParser.new do |opts|
-  opts.banner = "Usage: maf_tile [options] <maf> <index>"
+  opts.banner = "Usage: maf_tile [options] <maf> [index]"
   opts.separator ""
   opts.separator "Options:"
   opts.on("-r", "--reference SEQ", "FASTA reference sequence") do |ref|
     options.ref = ref
   end
-  opts.on("-i", "--interval BEGIN:END", "Genomic interval, zero-based") do |int|
-    if int =~ /(\d+):(\d+)/
+  opts.on("-i", "--interval [CHR:]BEGIN:END", "Genomic interval, zero-based") do |int|
+    if int =~ /(.+):(\d+):(\d+)/
+      gi = Bio::GenomicInterval.zero_based($1, ($2.to_i), ($3.to_i))
+      options.genomic_interval = gi
+    elsif int =~ /(\d+):(\d+)/
       options.interval = ($1.to_i)...($2.to_i)
     else
+      $stderr.puts "Invalid interval specification #{int}!"
       options.usage = true
     end
   end
@@ -51,30 +73,19 @@ maf_p = ARGV.shift
 index_p = ARGV.shift
 
 unless (! options.usage) \
-  && maf_p && index_p && (! options.species.empty?) \
-  && (options.output_base ? options.bed : options.interval)
+  && maf_p && (! options.species.empty?) \
+  && (options.output_base \
+      ? options.bed \
+      : options.interval || options.genomic_interval)
   $stderr.puts o_parser
   exit 2
 end
 
-tiler = Bio::MAF::Tiler.new
-tiler.index = Bio::MAF::KyotoIndex.open(index_p)
-tiler.parser = Bio::MAF::Parser.new(maf_p, options.p)
-tiler.reference = Bio::MAF::FASTARangeReader.new(options.ref) if options.ref
-tiler.species = options.species
-tiler.species_map = options.species_map
-
-def parse_interval(line)
-  src, r_start_s, r_end_s, _ = line.split(nil, 4)
-  r_start = r_start_s.to_i
-  r_end = r_end_s.to_i
-  return Bio::GenomicInterval.zero_based(src, r_start, r_end)
-end
-
-def target_for(base, interval)
-  path = "#{base}_#{interval.zero_start}-#{interval.zero_end}.fa"
-  File.open(path, 'w')
-end
+access = if File.directory? maf_p
+           Bio::MAF::Access.maf_dir(maf_p, options.p)
+         else
+           Bio::MAF::Access.file(maf_p, index_p, options.p)
+         end
 
 if options.bed
   intervals = []
@@ -83,21 +94,34 @@ if options.bed
   end
   intervals.sort_by! { |int| int.zero_start }
   intervals.each do |int|
-    tiler.interval = int
-    target = target_for(options.output_base, int)
-    tiler.write_fasta(target)
-    target.close
+    access.tile(int) do |tiler|
+      apply_options(options, tiler)
+      target_for(options.output_base, int) do |target|
+        tiler.write_fasta(target)
+      end
+    end
   end
 else
   # single interval
-  tiler.interval = Bio::GenomicInterval.zero_based(tiler.index.ref_seq,
-                                                   options.interval.begin,
-                                                   options.interval.end)
-  if options.output_base
-    target = target_for(options.output_base, tiler.interval)
+  if options.genomic_interval
+    interval = options.genomic_interval
   else
-    target = $stdout
+    if access.indices.size != 1
+      raise "Must explicitly specify sequence in --interval argument with multiple candidate MAF files!"
+    end
+    ref_seq = access.indices.keys.first
+    interval = Bio::GenomicInterval.zero_based(ref_seq,
+                                               options.interval.begin,
+                                               options.interval.end)
+  end
+  access.tile(interval) do |tiler|
+    apply_options(options, tiler)
+    if options.output_base
+      target = target_for(options.output_base, tiler.interval)
+    else
+      target = $stdout
+    end
+    tiler.write_fasta(target)
+    target.close
   end
-  tiler.write_fasta(target)
-  target.close
 end

data/bio-maf.gemspec

@@ -2,11 +2,11 @@
 
 Gem::Specification.new do |s|
   s.name = "bio-maf"
-  s.version = "0.2.0"
+  s.version = "0.3.0"
 
   s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
   s.authors = ["Clayton Wheeler"]
-  s.date = "2012-06-29"
+  s.date = "2012-07-18"
   s.description = "Multiple Alignment Format parser for BioRuby."
   s.email = "cswh@umich.edu"
   s.executables = ["maf_count", "maf_dump_blocks", "maf_extract_ranges_count", "maf_index", "maf_parse_bench", "maf_to_fasta", "maf_write", "random_ranges"]
@@ -32,10 +32,11 @@ Gem::Specification.new do |s|
     s.platform = 'java'
   end
 
+  s.add_runtime_dependency('bio-alignment', ["~> 0.0.7"])
   s.add_runtime_dependency('bio-bigbio', [">= 0"])
   s.add_runtime_dependency('bio-genomic-interval', ["~> 0.1.2"])
   if RUBY_PLATFORM == 'java'
-    s.add_runtime_dependency('kyotocabinet-java', ["~> 0.2.0"])
+    s.add_runtime_dependency('kyotocabinet-java', ["~> 0.3.0"])
   else    
     s.add_runtime_dependency('kyotocabinet-ruby', ["~> 1.27.1"])
   end

data/features/block-joining.feature

@@ -0,0 +1,32 @@
+Feature: Join adjacent alignment blocks
+  After filtering out sequences
+  The sequence that caused two blocks to be separate may be removed
+  So it can be desirable to join such blocks together
+
+  Scenario: Two blocks natively in indexed access
+    Given indexed MAF files in "test/data"
+    When I query for the genomic intervals
+    | chrom    | start    | end      |
+    | mm8.chr7 | 80082334 | 80082471 |
+    Then 2 blocks are obtained
+    And the text size of block 0 is 54
+    And the text size of block 1 is 156
+
+  Scenario: Two blocks joined in indexed access
+    Given indexed MAF files in "test/data"
+    When I enable the :join_blocks parser option
+    And I filter for only the species
+    | mm8     |
+    | rn4     |
+    | oryCun1 |
+    | hg18    |
+    | panTro2 |
+    | rheMac2 |
+    | canFam2 |
+    | loxAfr1 |
+    | echTel1 |
+    And I query for the genomic intervals
+    | chrom    | start    | end      |
+    | mm8.chr7 | 80082334 | 80082471 |
+    Then 1 block is obtained
+    And the text size of block 0 is 210

data/features/dir-access.feature

@@ -0,0 +1,46 @@
+Feature: Provide access to multiple MAF files in a directory
+  In order to efficiently work with many MAF files
+  We need to provide a convenient interface to them
+
+  Scenario: Query for several chromosomes at once
+    Given indexed MAF files in "test/data"
+    When I query for the genomic intervals
+    | chrom    | start    | end      |
+    | mm8.chr7 | 80082580 | 80082612 |
+    | mm8.chrM | 1400     | 1590     |
+    Then 5 blocks are obtained
+
+  Scenario: Apply block filters
+    Given indexed MAF files in "test/data"
+    When I filter for blocks with text size at most 200
+    And I query for the genomic intervals
+    | chrom    | start    | end      |
+    | mm8.chr7 | 80082580 | 80082612 |
+    | mm8.chrM | 1400     | 1590     |
+    Then 3 blocks are obtained
+
+  Scenario: Apply sequence filters
+    Given indexed MAF files in "test/data"
+    When I filter for only the species
+    | mm8  |
+    | rn4  |
+    | hg18 |
+    And I query for the genomic intervals
+    | chrom    | start    | end      |
+    | mm8.chr7 | 80082580 | 80082612 |
+    | mm8.chrM | 1400     | 1590     |
+    Then 5 blocks are obtained
+    And block 0 has 3 sequences
+
+  Scenario: Set parse options
+    Given indexed MAF files in "test/data"
+    When I enable the :remove_gaps parser option
+    And I filter for only the species
+    | mm8  |
+    | rn4  |
+    | hg18 |
+    And I query for the genomic intervals
+    | chrom    | start    | end      |
+    | mm8.chr7 | 80082580 | 80082612 |
+    Then 2 blocks are obtained
+    And the text size of block 1 is 121