bio-maf 0.1.0-java

data/bin/maf_to_fasta

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+#!/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_to_fasta [options] <maf> <fasta>"
+  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 |path|
+    options.ruby_prof = path
+  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
+end.parse!(ARGV)
+
+src_path = ARGV.shift
+dst_path = ARGV.shift
+
+if options.prof
+  require 'perftools'
+  PerfTools::CpuProfiler.start(options.prof)
+elsif options.ruby_prof
+  require 'ruby-prof'
+  RubyProf.start
+end
+
+if options.profile_gc
+  GC::Profiler.enable
+end
+
+parser = options.parser.new(src_path)
+writer = FastaWriter.new(dst_path)
+
+parser.each_block do |block|
+  block.each_raw_seq do |seq|
+    seq.write_fasta(writer)
+  end
+end
+
+writer.close
+
+if options.profile_gc
+  $stderr.puts GC::Profiler.result
+  GC::Profiler.disable
+end
+
+if options.prof
+  PerfTools::CpuProfiler.stop
+elsif options.ruby_prof
+  res = RubyProf.stop
+  printer = RubyProf::FlatPrinter.new(res)
+  File.open(options.ruby_prof, 'w') do |f|
+    printer.print(f)
+  end
+end

data/bin/maf_write

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+#!/usr/bin/env ruby
+
+require 'bio-maf'
+require 'optparse'
+require 'ostruct'
+
+options = OpenStruct.new
+options.parser = Bio::MAF::Parser
+options.opts = {
+  :chunk_reader => Bio::MAF::ChunkReader,
+  :parse_extended => false
+}
+
+PRINTERS = {
+  'flat' => :FlatPrinter,
+  'stack' => :CallStackPrinter
+}
+
+OptionParser.new do |opts|
+  opts.banner = "Usage: maf_write [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 = $2
+    else
+      options.ruby_prof_printer = RubyProf::FlatPrinter
+      options.ruby_prof_path = pspec
+    end
+  end
+  opts.on("--profile-gc", "Profile GC") do |prof|
+    options.profile_gc = true
+  end
+  opts.on("--parser PARSER", "parser") do |name|
+    options.parser = Bio::MAF.const_get(name)
+  end
+  opts.on("-t", "--threaded") do
+    options.opts[:chunk_reader] = Bio::MAF::ThreadedChunkReader
+    options.opts[:threads] = 1
+  end
+  opts.on("-e", "--extended") do
+    options.opts[:parse_extended] = true
+    options.opts[:parse_empty] = true
+  end
+end.parse!(ARGV)
+
+src_path = ARGV.shift
+
+if options.prof
+  require 'perftools'
+  PerfTools::CpuProfiler.start(options.prof)
+elsif options.ruby_prof_path
+  require 'ruby-prof'
+  RubyProf.start
+end
+
+if options.profile_gc
+  GC::Profiler.enable
+end
+
+parser = options.parser.new(src_path, options.opts)
+writer = Bio::MAF::Writer.new($stdout)
+writer.write_header(parser.header)
+writer.write_blocks(parser.parse_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/random_ranges

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+#!/usr/bin/env ruby
+
+require 'optparse'
+require 'ostruct'
+
+options = OpenStruct.new
+
+op = OptionParser.new do |opts|
+  opts.banner = "Usage: random_ranges [options]"
+  opts.on("-r", "--range START:END", "range") do |range|
+    s, e = range.split(':')
+    options.start = s.to_i
+    options.end = e.to_i
+  end
+  opts.on("-l", "--length LEN", "block length") do |len|
+    options.length = len.to_i
+  end
+  opts.on("-n", "--number NUM", "number of blocks") do |num|
+    options.num = num.to_i
+  end
+  opts.on("-s", "--sequence SEQ", "sequence") do |seq|
+    options.seq = seq
+  end
+end.parse!(ARGV)
+
+rand = Random.new
+range = options.end - options.start
+block_range = range / options.num
+block_start_range = block_range - options.length
+(0...options.num).each do |n|
+  block_offset = rand.rand(block_start_range)
+  b_start = options.start + (block_range * n) + block_offset
+  b_end = b_start + options.length
+  puts "#{options.seq}\t#{b_start}\t#{b_end}\tx"
+end

data/features/maf-indexing.feature

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+@milestone_2
+Feature: Indexed access to MAF files
+  In order to extract alignment blocks from MAF files
+  By chromosomal ranges matching a source sequence
+  I want to have a way to build indexes on MAF files
+  And use indexes to efficiently find alignment blocks
+  Because linear searches of a 200 GB file are impractical
+
+  Scenario: Index a MAF file
+    Given a MAF source file "mm8_chr7_tiny.maf"
+    When I open it with a MAF reader
+    And build an index on the reference sequence
+    Then the index has at least 8 entries
+    
+  Scenario: Extract alignment blocks by chromosomal range
+    Given a MAF source file "mm8_chr7_tiny.maf"
+    When I open it with a MAF reader
+    And build an index on the reference sequence
+    And search for blocks between positions 80082592 and 80082766 of mm8.chr7
+    Then 2 blocks are obtained
+    And sequence mm8.chr7 of block 0 has start 80082592
+    And sequence mm8.chr7 of block 1 has start 80082713
+    
+  Scenario: Extract alignment blocks by chromosomal range from index file
+    Given a MAF source file "mm8_chr7_tiny.maf"
+    And a Kyoto Cabinet index file "mm8_chr7_tiny.kct"
+    When I open it with a MAF reader
+    And search for blocks between positions 80082592 and 80082766 of mm8.chr7
+    Then 2 blocks are obtained
+    And sequence mm8.chr7 of block 0 has start 80082592
+    And sequence mm8.chr7 of block 1 has start 80082713

data/features/maf-output.feature

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+Feature: MAF output
+  In order to output modified MAF files or subsets of them
+  I want to be able to write out parsed MAF data
+
+  Scenario: Reproduce simple test data
+    Given a MAF source file "mm8_single.maf"
+    When I open it with a MAF reader
+    And open a new MAF writer
+    And write the header from the original MAF file
+    And write all the parsed blocks
+    Then the output should match, except whitespace, "mm8_single.maf"
+
+  Scenario: Reproduce longer test data
+    Given a MAF source file "mm8_chr7_tiny.maf"
+    When I open it with a MAF reader
+    And open a new MAF writer
+    And write the header from the original MAF file
+    And write all the parsed blocks
+    Then the output should match, except whitespace, "mm8_chr7_tiny.maf"
+
+  Scenario: Reproduce test data with i, e, q lines
+    Given a MAF source file "chr22_ieq.maf"
+    When I enable the :parse_extended parser option
+    And I enable the :parse_empty parser option
+    And I open it with a MAF reader
+    And open a new MAF writer
+    And write the header from the original MAF file
+    And write all the parsed blocks
+    Then the output should match, except whitespace, "chr22_ieq.maf"

data/features/maf-parsing.feature

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+Feature: Parse MAF files
+  In order to extract information from a MAF file
+  I want to read it and pull out information
+
+  Scenario: Read MAF header
+    Given MAF data:
+    """
+    ##maf version=1 scoring=humor.v4
+    # humor.v4 R=30 M=10 /cluster/data/hg15/bed/blastz.mm3/axtNet25/chr22.maf /cluster/data/hg15/bed/blastz.rn3/axtNet25/chr22.maf
+
+    a score=0.128
+    s human_hoxa 100  8 + 100257 ACA-TTACT
+    s horse_hoxa 120  9 -  98892 ACAATTGCT
+    s fugu_hoxa   88  7  + 90788 ACA--TGCT
+    """
+    When I open it with a MAF reader
+    Then the MAF version should be "1"
+    And the scoring scheme should be "humor.v4"
+    # third line a continuation
+    And the alignment parameters should be "humor.v4 R=30 M=10 /cluster/data/hg15/bed/blastz.mm3/axtNet25/chr22.maf /cluster/data/hg15/bed/blastz.rn3/axtNet25/chr22.maf" 
+
+  Scenario: Read alignment block
+    Given MAF data:
+    """
+    ##maf version=1 scoring=humor.v4
+    # humor.v4 R=30 M=10 /cluster/data/hg15/bed/blastz.mm3/axtNet300/chr1.maf
+    # /cluster/data/hg15/bed/blastz.rn3/axtNet300/chr1.maf
+
+    a score=0.128
+    s human_hoxa 100  8 + 100257 ACA-TTACT
+    s horse_hoxa 120  9 -  98892 ACAATTGCT
+    s fugu_hoxa   88  7  + 90788 ACA--TGCT
+    """
+    When I open it with a MAF reader
+    Then an alignment block can be obtained
+    And the alignment block has 3 sequences
+    And sequence 0 has source "human_hoxa"
+    And sequence 0 has start 100
+    And sequence 0 has size 8
+    And sequence 0 has strand :+
+    And sequence 0 has source size 100257
+    And sequence 0 has text "ACA-TTACT"
+    And sequence 1 has strand :-
+

data/features/maf-querying.feature

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+@milestone_3
+Feature: Filter results from MAF files
+  In order to work with only relevant data from a MAF file
+  Such as only species recognized by PhyloCSF
+  I want to filter the results of MAF queries
+
+  Scenario: Return only specified species
+    Given MAF data:
+    """
+    ##maf version=1
+    a score=10542.0
+    s mm8.chr7                 80082334 34 + 145134094 GGGCTGAGGGC--AGGGATGG---AGGGCGGTCC--------------CAGCA- 
+    s rn4.chr1                136011785 34 + 267910886 GGGCTGAGGGC--AGGGACGG---AGGGCGGTCC--------------CAGCA- 
+    s oryCun1.scaffold_199771     14021 43 -     75077 -----ATGGGC--AAGCGTGG---AGGGGAACCTCTCCTCCCCTCCGACAAAG- 
+    s hg18.chr15               88557580 27 + 100338915 --------GGC--AAGTGTGGA--AGGGAAGCCC--------------CAGAA- 
+    s panTro2.chr15            87959837 27 + 100063422 --------GGC--AAGTGTGGA--AGGGAAGCCC--------------CAGAA- 
+    s rheMac2.chr7             69864714 28 + 169801366 -------GGGC--AAGTATGGA--AGGGAAGCCC--------------CAGAA- 
+    s canFam2.chr3             56030570 39 +  94715083 AGGTTTAGGGCAGAGGGATGAAGGAGGAGAATCC--------------CTATG- 
+    s dasNov1.scaffold_106893      7435 34 +      9831 GGAACGAGGGC--ATGTGTGG---AGGGGGCTGC--------------CCACA- 
+    s loxAfr1.scaffold_8298       30264 38 +     78952 ATGATGAGGGG--AAGCGTGGAGGAGGGGAACCC--------------CTAGGA 
+    s echTel1.scaffold_304651       594 37 -     10007 -TGCTATGGCT--TTGTGTCTAGGAGGGGAATCC--------------CCAGGA 
+    """
+    When I open it with a MAF reader
+    And filter for only the species
+    | hg18    |
+    | mm8     |
+    | rheMac2 |
+    Then an alignment block can be obtained
+    And the alignment block has 3 sequences
+
+  Scenario: Return only blocks having all specified species
+    Given a MAF source file "mm8_chr7_tiny.maf"
+    When I open it with a MAF reader
+    And build an index on the reference sequence
+    And filter for blocks with the species
+    | panTro2 |
+    | loxAfr1 |
+    And search for blocks between positions 80082471 and 80082730 of mm8.chr7
+    Then 1 block is obtained
+
+  Scenario: Return only blocks having a certain number of sequences
+    Given a MAF source file "mm8_chr7_tiny.maf"
+    When I open it with a MAF reader
+    And build an index on the reference sequence
+    And filter for blocks with at least 6 sequences
+    And search for blocks between positions 80082767 and 80083008 of mm8.chr7
+    Then 1 block is obtained
+
+  # sizes present:
+  # 55 64 128 148 157 163 165 192 
+
+  Scenario: Return blocks with a maximum text size
+    Given a MAF source file "mm8_chr7_tiny.maf"
+    When I open it with a MAF reader
+    And build an index on the reference sequence
+    And filter for blocks with text size at least 150
+    And search for blocks between positions 0 and 80100000 of mm8.chr7
+    Then 4 blocks are obtained
+
+  Scenario: Return blocks with a minimum text size
+    Given a MAF source file "mm8_chr7_tiny.maf"
+    When I open it with a MAF reader
+    And build an index on the reference sequence
+    And filter for blocks with text size at most 72
+    And search for blocks between positions 0 and 80100000 of mm8.chr7
+    Then 2 blocks are obtained
+
+  Scenario: Return blocks within a text size range
+    Given a MAF source file "mm8_chr7_tiny.maf"
+    When I open it with a MAF reader
+    And build an index on the reference sequence
+    And filter for blocks with text size between 72 and 160
+    And search for blocks between positions 0 and 80100000 of mm8.chr7
+    Then 3 blocks are obtained
+

data/features/maf-to-fasta.feature

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+Feature: Convert MAF file to FASTA
+  In order to use multiple alignment data with other tools
+  I want to read a Multiple Alignment Format (MAF) file and write out its data as FASTA
+
+  Scenario: Convert simple MAF file
+    Given a MAF source file "t1.maf"
+    When I select FASTA output
+    And I open it with a MAF reader
+    And process the file
+    Then the output should match "t1.fasta"
+
+  Scenario: Convert simple MAF data
+    Given MAF data:
+    """
+    ##maf version=1 scoring=humor.v4
+    # humor.v4 R=30 M=10 /cluster/data/hg15/bed/blastz.mm3/axtNet300/chr1.maf
+    # /cluster/data/hg15/bed/blastz.rn3/axtNet300/chr1.maf
+
+    a score=0.128
+    s human_hoxa 100  8 + 100257 ACA-TTACT
+    s horse_hoxa 120  9 -  98892 ACAATTGCT
+    s fugu_hoxa   88  7  + 90788 ACA--TGCT
+
+
+    a score=0.071
+    s human_unc 9077 8 + 10998 ACAGTATT
+    # Comment
+    s horse_unc 4555 6 -  5099 ACA--ATT
+    s fugu_unc  4000 4 +  4038 AC----TT
+    """
+    When I select FASTA output
+    And I open it with a MAF reader
+    And process the file
+    Then the output should be:
+    """
+    >human_hoxa:100-108
+    ACA-TTACT
+    >horse_hoxa:120-129
+    ACAATTGCT
+    >fugu_hoxa:88-95
+    ACA--TGCT
+    >human_unc:9077-9085
+    ACAGTATT
+    >horse_unc:4555-4561
+    ACA--ATT
+    >fugu_unc:4000-4004
+    AC----TT
+    
+    """
+

data/features/step_definitions/convert_steps.rb

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+require 'bigbio'                # FASTA support
+
+Given /^a MAF source file "(.*?)"$/ do |src|
+  @src_f = $test_data + src
+  @src_f.exist?.should be_true
+end
+
+Given /^MAF data:$/ do |string|
+  @src_f = Tempfile.new(['rspec', '.maf'])
+  @src_f.write(string)
+  @src_f.close
+end
+
+When /^I select FASTA output$/ do
+  @dst = Tempfile.new(['cuke', ".#{@out_fmt.to_s}"])
+  @dst.close
+  @writer = FastaWriter.new(@dst.path)
+end
+
+When /^process the file$/ do
+  @parser.each_block do |block|
+    block.each_raw_seq do |seq|
+      seq.write_fasta(@writer)
+    end
+  end
+  @writer.close
+end
+
+Then /^the output should match "(.*?)"$/ do |ref|
+  ref_p = $test_data + ref
+  ref_p.exist?.should be_true
+  #system("diff #{ref} #{@dst.path} >/dev/null 2>&1").should be_true
+  File.read(@dst.path).should == File.read(ref_p)
+end
+
+Then /^the output should be:$/ do |string|
+  File.read(@dst.path).should == string
+end
+
+After do
+  if @dst
+    @dst.close
+    @dst.unlink
+  end
+end