bio-maf 0.1.0-java

data/benchmarks/iter_bench

@@ -0,0 +1,44 @@
+#!/usr/bin/env ruby
+
+require 'benchmark'
+
+n = 1000000
+data = <<EOF
+a score=28680.000000
+s hg19.chr22                    16050711 61 + 51304566 atctccaagagggcataaaacac-tgagtaaacagctcttttatatgtgtttcctggatgag
+s panTro2.chrUn                  7681110 59 + 58616431 atctccaagagggcataaaacac-tgagtaaacagctctt--atatgtgtttcctggatgag
+q panTro2.chrUn                                        99999999999999999999999-9999999999999999--99999999999999999999
+i panTro2.chrUn                 C 0 C 0
+s tarSyr1.scaffold_75923            2859 50 -     8928 atctccaagagggctgaaaatgc-caaatga-----------tcacacgtttcctggacaag
+q tarSyr1.scaffold_75923                               79295966999999999999998-9999799-----------99999999997657759999
+i tarSyr1.scaffold_75923        N 0 C 0
+s micMur1.scaffold_22105            5493 59 -    10683 acctccgagagggctcaaaacgc-cgagtgatcagctctt--atgcgcgtttcctggacgag
+q micMur1.scaffold_22105                               99999999999999999999999-9999999999999999--99999999999999999999
+i micMur1.scaffold_22105        C 0 C 0
+s tupBel1.scaffold_3803.1-85889    33686 61 +    85889 ttcaggaagggggcccaaaacgcttgagtggtcagctctta-ttttgcgtttactggatggg
+q tupBel1.scaffold_3803.1-85889                        79648579699867994997775679665662767577569-69987455976776322888
+i tupBel1.scaffold_3803.1-85889 I 1 C 0
+s vicPac1.scaffold_12713            6831 55 -    10681 actgccatgggggctcagcgtac-tgaatggttaattact------gtggtccccgaatgag
+q vicPac1.scaffold_12713                               99999999999999999999999-9999999999999999------9999999999999999
+EOF
+
+Benchmark.bmbm do |x|
+  x.report("split/each") do
+    n.times do
+      i = 0
+      data.split("\n").each do |line|
+        i += line.size
+      end
+    end
+  end
+  x.report("until/shift") do
+    n.times do
+      i = 0
+      lines = data.split("\n")
+      until lines.empty?
+        line = lines.shift
+        i += line.size
+      end
+    end
+  end
+end

data/benchmarks/read_bench

@@ -0,0 +1,40 @@
+#!/usr/bin/env ruby
+
+require 'benchmark'
+
+FILE = '/Users/csw/maf/chr22.maf'
+
+Benchmark.bm do |x|
+  x.report("8k") do
+    File.open(FILE) do |f|
+      while true
+        r = f.read(8192)
+        break unless r
+      end
+    end
+  end
+  x.report("128k") do
+    File.open(FILE) do |f|
+      while true
+        r = f.read(128 * 1024)
+        break unless r
+      end
+    end
+  end
+  x.report("1M") do
+    File.open(FILE) do |f|
+      while true
+        r = f.read(1024 * 1024)
+        break unless r
+      end
+    end
+  end
+  x.report("8M") do
+    File.open(FILE) do |f|
+      while true
+        r = f.read(8 * 1024 * 1024)
+        break unless r
+      end
+    end
+  end
+end

data/benchmarks/sort_bench

@@ -0,0 +1,33 @@
+#!/usr/bin/env ruby
+
+require 'benchmark'
+
+class Thing
+  attr_reader :part
+
+  def initialize(part)
+    @part = part
+  end
+end
+
+prng = Random.new
+v_max = 1 << 31
+ary = []
+1000.times do
+  ary << Thing.new(rand(v_max))
+end
+
+Benchmark.bmbm do |x|
+  x.report("sort!") do
+    1000.times do
+      ary2 = ary.dup
+      ary2.sort! { |a, b| a.part <=> b.part }
+    end
+  end
+  x.report("sort_by!") do
+    1000.times do
+      ary2 = ary.dup
+      ary2.sort_by! { |i| i.part }
+    end
+  end
+end

data/benchmarks/split_bench

@@ -0,0 +1,33 @@
+#!/usr/bin/env ruby
+
+require 'benchmark'
+
+n = 2000000
+line = 's tupBel1.scaffold_3803.1-85889    33686 61 +    85889 ttcaggaagggggcccaaaacgcttgagtggtcagctctta-ttttgcgtttactggatggg'
+
+Benchmark.bmbm do |x|
+  x.report("basic String#split") do
+    n.times do
+      parts = line.split
+    end
+  end
+  x.report("regex split") do
+    n.times do
+      parts = line.split(/\s+/)
+    end
+  end
+  x.report("regex fields") do
+    n.times do
+      if m = /^s\s+(\S+)\s+(\d+)\s+(\d+)\s+([+-])\s+(\d+)\s+(\S+)/.match(line)
+        parts = m.captures
+      end
+    end
+  end
+  x.report("regex fields") do
+    n.times do
+      if m = /^s\s+(\S+)\s+(\d+)\s+(\d+)\s+([+-])\s+(\d+)\s+(\S+)/.match(line)
+        parts = m.captures
+      end
+    end
+  end
+end

data/bin/maf_count

@@ -0,0 +1,82 @@
+#!/usr/bin/env ruby
+
+require 'bio-maf'
+require 'bigbio'
+require 'optparse'
+require 'ostruct'
+
+options = OpenStruct.new
+options.parser = Bio::MAF::Parser
+options.reader = Bio::MAF::ChunkReader
+
+PRINTERS = {
+  'flat' => :FlatPrinter,
+  'stack' => :CallStackPrinter
+}
+
+OptionParser.new do |opts|
+  opts.banner = "Usage: maf_count [options] <maf>"
+  opts.separator ""
+  opts.separator "Options:"
+  opts.on("-p", "--profile PROF", "Profile with PerfTools") do |prof|
+    options.prof = prof
+  end
+  opts.on("--ruby-prof PATH", "Profile with ruby-prof") do |pspec|
+    if pspec =~ /(\w+):(.+)/
+      require 'ruby-prof'
+      options.ruby_prof_printer = RubyProf.const_get(PRINTERS.fetch($1))
+      options.ruby_prof_path = $2
+    else
+      options.ruby_prof_printer = RubyProf::FlatPrinter
+      options.ruby_prof_path = pspec
+    end
+  end
+  opts.on("--profile-gc", "Profile GC") do |prof|
+    options.profile_gc = true
+  end
+  opts.on("--parser PARSER", "parser") do |name|
+    options.parser = Bio::MAF.const_get(name)
+  end
+  opts.on("-t", "--threaded") do
+    options.reader = Bio::MAF::ThreadedChunkReader
+  end
+end.parse!(ARGV)
+
+src_path = ARGV.shift
+
+if options.prof
+  require 'perftools'
+  PerfTools::CpuProfiler.start(options.prof)
+elsif options.ruby_prof_path
+  require 'ruby-prof'
+  RubyProf.start
+end
+
+if options.profile_gc
+  GC::Profiler.enable
+end
+
+parser = options.parser.new(src_path,
+                            :chunk_reader => options.reader,
+                            :parse_extended => false)
+
+n = 0
+parser.each_block do |block|
+  n += 1
+end
+puts "Parsed #{n} MAF alignment blocks."
+
+if options.profile_gc
+  $stderr.puts GC::Profiler.result
+  GC::Profiler.disable
+end
+
+if options.prof
+  PerfTools::CpuProfiler.stop
+elsif options.ruby_prof_path
+  res = RubyProf.stop
+  printer = options.ruby_prof_printer.new(res)
+  File.open(options.ruby_prof_path, 'w') do |f|
+    printer.print(f)
+  end
+end

data/bin/maf_dump_blocks

@@ -0,0 +1,27 @@
+#!/usr/bin/env ruby
+
+require 'bio-maf'
+require 'bigbio'
+require 'optparse'
+require 'ostruct'
+
+options = OpenStruct.new
+options.parser = Bio::MAF::Parser
+
+OptionParser.new do |opts|
+  opts.banner = "Usage: maf_dump_blocks [options] <maf>"
+  opts.separator ""
+  opts.separator "Options:"
+  opts.on("--parser PARSER", "parser") do |name|
+    options.parser = Bio::MAF.const_get(name)
+  end
+end.parse!(ARGV)
+
+src_path = ARGV.shift
+
+parser = options.parser.new(src_path)
+
+parser.each_block do |block|
+  $stdout.printf("%12d\t%7d\n", block.offset, block.size)
+end
+

data/bin/maf_extract_ranges_count

@@ -0,0 +1,44 @@
+#!/usr/bin/env ruby
+
+require 'optparse'
+require 'ostruct'
+
+require 'bio-maf'
+require 'bio-genomic-interval'
+
+options = OpenStruct.new
+options.p = { :threads => 1 }
+options.passes = 1
+
+OptionParser.new do |opts|
+  opts.banner = "Usage: maf_extract_ranges_count [options] <maf> <index>"
+  opts.separator ""
+  opts.separator "Options:"
+  opts.on("-t", "--threads N", "Parser threads") do |n|
+    options.p[:threads] = n.to_i
+  end
+  opts.on("-p", "--passes N", "Number of passes") do |n|
+    options.passes = n.to_i
+  end
+end.parse!(ARGV)
+
+maf_p = ARGV.shift
+index_p = ARGV.shift
+
+parser = Bio::MAF::Parser.new(maf_p, options.p)
+index = Bio::MAF::KyotoIndex.open(index_p)
+
+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
+
+intervals = []
+$stdin.each_line { |line| intervals << parse_interval(line) }
+
+options.passes.times do
+  blocks = index.find(intervals, parser)
+  puts "TOTAL: #{blocks.count} blocks parsed."
+end

data/bin/maf_index

@@ -0,0 +1,88 @@
+#!/usr/bin/env ruby
+
+require 'benchmark'
+require 'bio-maf'
+require 'optparse'
+require 'ostruct'
+
+PRINTERS = {
+  'flat' => :FlatPrinter,
+  'stack' => :CallStackPrinter,
+  'graph' => :GraphHtmlPrinter
+}
+
+$options = OpenStruct.new
+$options.mode = :build
+$options.reader = Bio::MAF::ChunkReader
+
+def build_index(maf, index)
+  parser = Bio::MAF::Parser.new(maf,
+                                :chunk_reader => $options.reader,
+                                :parse_extended => false)
+  idx = Bio::MAF::KyotoIndex.build(parser, index)
+  idx.close
+end
+
+op = OptionParser.new do |opts|
+  opts.banner = "Usage: maf_index [options] <maf> <index>"
+  #opts.separator ""
+  #opts.separator "Options:"
+  opts.on("--time", "print elapsed time") do
+    $options.bench = true
+  end
+  opts.on("-d", "--dump") do
+    $options.mode = :dump
+  end
+  opts.on("-t", "--threaded") do
+    $options.reader = Bio::MAF::ThreadedChunkReader
+  end
+  opts.on("--ruby-prof PATH", "Profile with ruby-prof") do |pspec|
+    require 'ruby-prof'
+    if pspec =~ /(\w+):(.+)/
+      $options.ruby_prof_printer = RubyProf.const_get(PRINTERS.fetch($1))
+      $options.ruby_prof_path = $2
+    else
+      $options.ruby_prof_printer = Ruby_Prof::FlatPrinter
+      $options.ruby_prof_path = pspec
+    end
+  end
+end
+
+op.parse!(ARGV)
+
+maf_p = ARGV.shift if $options.mode == :build
+index_p = ARGV.shift
+
+unless (maf_p || $options.mode == :dump) && index_p
+  $stderr.puts op
+  exit 1
+end
+
+if $options.ruby_prof_path
+  RubyProf.start
+end
+
+case $options.mode
+when :build
+  if ! $options.bench
+    build_index(maf_p, index_p)
+  else
+    bm_res = Benchmark.measure do
+      build_index(maf_p, index_p)
+    end
+    puts bm_res
+  end
+when :dump
+  idx = Bio::MAF::KyotoIndex.open(index_p)
+  idx.dump
+else
+  raise "Unsupported mode: #{$options.mode}"
+end
+
+if $options.ruby_prof_path
+  res = RubyProf.stop
+  printer = $options.ruby_prof_printer.new(res)
+  File.open($options.ruby_prof_path, 'w') do |f|
+    printer.print(f)
+  end
+end

data/bin/maf_parse_bench

@@ -0,0 +1,94 @@
+#!/usr/bin/env ruby
+
+require 'benchmark'
+require 'bio-maf'
+require 'optparse'
+require 'ostruct'
+
+options = OpenStruct.new
+options.parser = Bio::MAF::Parser
+options.runs = 100_000
+options.warmup = false
+
+PRINTERS = {
+  'flat' => :FlatPrinter,
+  'stack' => :CallStackPrinter
+}
+
+OptionParser.new do |opts|
+  opts.banner = "Usage: maf_parse_bench [options] <maf>"
+  opts.separator ""
+  opts.separator "Options:"
+  opts.on("-p", "--profile PROF", "Profile with PerfTools") do |prof|
+    options.prof = prof
+  end
+  opts.on("--ruby-prof PATH", "Profile with ruby-prof") do |pspec|
+    if pspec =~ /(\w+):(.+)/
+      require 'ruby-prof'
+      options.ruby_prof_printer = RubyProf.const_get(PRINTERS.fetch($1))
+      options.ruby_prof_path = $2
+    else
+      options.ruby_prof_printer = :FlatPrinter
+      options.ruby_prof_path = pspec
+    end
+  end
+  opts.on("--profile-gc", "Profile GC") do |prof|
+    options.profile_gc = true
+  end
+  opts.on("--parser PARSER", "parser") do |name|
+    options.parser = Bio::MAF.const_get(name)
+  end
+  opts.on("-w", "--warmup", "perform warmup run") do 
+    options.warmup = true
+  end
+end.parse!(ARGV)
+
+src_path = ARGV.shift
+
+if options.prof
+  require 'perftools'
+  PerfTools::CpuProfiler.start(options.prof)
+elsif options.ruby_prof_path
+  require 'ruby-prof'
+  RubyProf.start
+end
+
+if options.profile_gc
+  GC::Profiler.enable
+end
+
+parser = options.parser.new(src_path)
+parser.parse_block
+parser.parse_block
+pos = parser.s.pos
+
+if options.warmup
+  options.runs.times do
+    parser.parse_block
+    parser.s.pos = pos
+  end
+end
+
+bm_res = Benchmark.measure do
+  options.runs.times do
+    parser.parse_block
+    parser.s.pos = pos
+  end
+end
+
+if options.profile_gc
+  $stderr.puts GC::Profiler.result
+  GC::Profiler.disable
+end
+
+if options.prof
+  PerfTools::CpuProfiler.stop
+elsif options.ruby_prof_path
+  res = RubyProf.stop
+  printer = options.ruby_prof_printer.new(res)
+  File.open(options.ruby_prof_path, 'w') do |f|
+    printer.print(f)
+  end
+end
+
+puts bm_res / options.runs