bio-maf 0.1.0

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

data/features/step_definitions/index_steps.rb

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+When /^build an index on the reference sequence$/ do
+  @idx = Bio::MAF::KyotoIndex.build(@parser, '%')
+end
+
+Given /^a Kyoto Cabinet index file "(.*?)"$/ do |name|
+  @idx = Bio::MAF::KyotoIndex.open($test_data + name)
+end
+
+Then /^the index has at least (\d+) entries$/ do |size_spec|
+  @idx.db.count.should be >= size_spec.to_i
+end
+
+When /^search for blocks between positions (\d+) and (\d+) of (\S+)$/ do |i_start, i_end, chr|
+  int = Bio::GenomicInterval.zero_based(chr, i_start.to_i, i_end.to_i)
+  @blocks = @idx.find([int], @parser, @block_filter).to_a
+end
+
+Then /^(\d+) blocks? (?:is|are) obtained$/ do |num|
+  @blocks.size.should == num.to_i
+end

data/features/step_definitions/output_steps.rb

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+When /^open a new MAF writer$/ do
+  @dst = Tempfile.new(["cuke", ".maf"])
+  @writer = Bio::MAF::Writer.new(@dst)
+end
+
+When /^write the header from the original MAF file$/ do
+  @writer.write_header(@parser.header)
+end
+
+When /^write all the parsed blocks$/ do
+  @writer.write_blocks(@parser.parse_blocks)
+end
+
+RSpec::Matchers.define :match_except_ws do |expected|
+  match do |actual|
+    system("diff --ignore-space-change --brief #{expected} #{actual} >/dev/null 2>&1")
+  end
+
+  failure_message_for_should do |actual|
+    msg = "File contents did not match. Diff:\n"
+    msg << `diff --unified --ignore-space-change #{expected} #{actual}`
+  end
+end
+
+Then /^the output should match, except whitespace, "(.+)"$/ do |ref|
+  @dst.path.should match_except_ws($test_data + ref)
+end

data/features/step_definitions/parse_steps.rb

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+When /^I open it with a MAF reader$/ do
+  @parser = Bio::MAF::Parser.new(@src_f, @opts || {})
+end
+
+When /^I enable the :(\S+) parser option$/ do |opt_s|
+  @opts ||= {}
+  @opts[opt_s.to_sym] = true
+end
+
+Then /^the MAF version should be "(.*?)"$/ do |v_spec|
+  @parser.header.version.to_s.should == v_spec
+end
+
+Then /^the scoring scheme should be "(.*?)"$/ do |s_spec|
+  @parser.header.scoring.should == s_spec
+end
+
+Then /^the alignment parameters should be "(.*?)"$/ do |a_spec|
+  @parser.header.alignment_params.should == a_spec
+end
+
+Then /^an alignment block can be obtained$/ do
+  @block = @parser.parse_block
+  @block.should_not be_nil
+end
+
+Then /^the alignment block has (\d+) sequences$/ do |n_seq|
+  @block.sequences.size.should == n_seq.to_i
+end
+
+Then /^sequence (\d+) has (\w.*?) "(.*?)"$/ do |i, method, str|
+  method_sym = method.gsub(/ /, '_').to_sym
+  @block.raw_seq(i.to_i).send(method_sym).should == str
+end
+
+Then /^sequence (\d+) has (\w.*?) (\d+)\s*$/ do |i, method, num|
+  method_sym = method.gsub(/ /, '_').to_sym
+  @block.raw_seq(i.to_i).send(method_sym).should == num.to_i
+end
+
+Then /^sequence (\d+) has (\w.*?) :(\S+)\s*$/ do |i, method, sym_s|
+  method_sym = method.gsub(/ /, '_').to_sym
+  value_sym = sym_s.to_sym
+  @block.raw_seq(i.to_i).send(method_sym).should == value_sym
+end
+
+Then /^sequence (\S+) of block (\d+) has (\w.*?) "(.*?)"$/ do |chr, i, method, str|
+  seq = @blocks[i.to_i].sequences.find { |seq| seq.source == chr }
+  method_sym = method.gsub(/ /, '_').to_sym
+  seq.send(method_sym).should == str
+end
+
+Then /^sequence (\S+) of block (\d+) has (\w.*?) (\d+)$/ do |chr, i, method, num|
+  seq = @blocks[i.to_i].sequences.find { |seq| seq.source == chr }
+  method_sym = method.gsub(/ /, '_').to_sym
+  seq.send(method_sym).should == num.to_i
+end
+
+Then /^sequence (\S+) of block (\d+) has (\w.*?) :(\S+)$/ do |chr, i, method, sym_s|
+  seq = @blocks[i.to_i].sequences.find { |seq| seq.source == chr }
+  method_sym = method.gsub(/ /, '_').to_sym
+  seq.send(method_sym).should == sym_s.to_sym
+end

data/features/step_definitions/query_steps.rb

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+When /^filter for only the species$/ do |table|
+  # table is a Cucumber::Ast::Table
+  sp = table.raw.collect { |row| row[0] }
+  @parser.sequence_filter = { :only_species => sp }
+end
+
+When /^filter for blocks with the species$/ do |table|
+  # table is a Cucumber::Ast::Table
+  sp = table.raw.collect { |row| row[0] }
+  @block_filter = { :with_all_species => sp }
+end
+
+When /^filter for blocks with at least (\d+) sequences$/ do |n|
+  @block_filter = { :at_least_n_sequences => n.to_i }
+end
+
+When /^filter for blocks with text size at (least|most) (\d+)$/ do |op, len|
+  constraint = case op
+               when 'least' then :min_size
+               when 'most' then :max_size
+               else raise "bad operator #{op}!"
+               end
+  @block_filter = { constraint => len.to_i}
+end
+
+When /^filter for blocks with text size between (\d+) and (\d+)$/ do |min, max|
+  @block_filter = {
+    :min_size => min.to_i,
+    :max_size => max.to_i
+  }
+end

data/features/step_definitions/ucsc_bin_steps.rb

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+#require 'bio-ucsc-api'
+
+Given /^I have a region with start (\d+) and end (\d+)$/ do |r_start, r_end|
+  @r_start = r_start.to_i
+  @r_end = r_end.to_i
+end
+
+When /^I compute the smallest containing bin$/ do
+  @bin = Bio::Ucsc::UcscBin.bin_from_range(@r_start, @r_end)
+end
+
+Then /^the bin should be (\d+)$/ do |expected_bin|
+  @bin.should == expected_bin.to_i
+end

data/features/support/env.rb

@@ -0,0 +1,16 @@
+unless ENV.has_key?('TRAVIS') || RUBY_PLATFORM == 'java'
+  begin
+    require 'simplecov'
+  rescue LoadError
+    $stderr.puts "WARNING: could not require 'simplecov': #{$!}"
+  end
+end
+
+require 'pathname'
+require 'tempfile'
+
+$LOAD_PATH << File.expand_path('../../../lib', __FILE__)
+
+require 'bio-maf'
+
+$test_data = Pathname.new 'test/data'

data/features/ucsc-bins.feature

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+Feature: Computation of UCSC bins
+  In order to efficiently use indexes
+  We will use the UCSC bin indexing system
+  Per http://genomewiki.ucsc.edu/index.php/Bin_indexing_system
+
+  Scenario Outline: Compute smallest containing bin
+    Given I have a region with start <Start> and end <End>
+    When I compute the smallest containing bin
+    Then the bin should be <Bin>
+
+    Examples:
+    |    Start |      End |  Bin |
+    | 25079603 | 25079787 |  776 |
+    | 25128173 | 25128248 |  776 |
+    | 50312474 | 50312703 |  968 |
+    | 41905591 | 41906101 |  904 |
+    | 16670899 | 16673060 |  712 |
+    | 75495356 | 75495494 | 1160 |
+    | 92259501 | 92261053 | 1288 |
+    | 83834063 | 83838132 | 1224 |
+    |  7309597 |  7310411 |  640 |
+    |  6190410 |  6190999 |  632 |
+    # from https://github.com/polyatail/biopython/blob/af34c033d78c4c72dffbb500e513e568a2ba5e29/Tests/test_MafIO_index.py#L48
+