bio-mummer 0.2.0 → 0.2.1

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 37345c73287e9b80c15dc7426ee1045caad772f7
-  data.tar.gz: 8b57b1755f5da0ba52af5ccbb92c3d55f06964e5
+  metadata.gz: 299d153188c65b1881bf1635b7389276ab1733f2
+  data.tar.gz: 3e3bf43c9c1551715d82c40bfd6c1b151f58dc2f
 SHA512:
-  metadata.gz: c86e8bb5d957da2331d817101577aa9990e4685a6445d5b194747c069fc8d5708b93465e20ff95b4e1a37de9ab02402552c1d77a7ba1acd98ddbeb61bb98d574
-  data.tar.gz: ffb5c859d7add8bb10c9d0a8dc5dc98a51dcb9a06370633d7fe6d69a3bd8d295836bafe4e32796ba6b62a855cde9a224731aa1c1cf45e077e8cc21eb4c31fb84
+  metadata.gz: c397099eb1478ceb5bc65d9657c64cfbe1bd02d2d0ce8e91a878065d1cf24407553d2f9609f8102af8b361d30b9048a499c4863a2b0772462f1977ae7d4d75ea
+  data.tar.gz: 3b1cdf0711552be2cdbfb3d1ad309d5d8abcdf7bbdae096cbcf439c6a9da2bba181b1085088ff4e1dcf1f8f84839186337977b048f7a89700b8c800717c71501

data/VERSION

@@ -1 +1 @@
-0.2.0
+0.2.1

data/bin/delta2gvcf.rb

@@ -20,6 +20,7 @@ class OptParser
       opts.on("-d", "--delta FILENAME", "Delta file generated by nucmer") do |fn|
         pn = Pathname.new(fn)
         if pn.size?
+          options.samplename = pn.basename(".delta")
           options.delta = pn
           match = pn.each_line.first.match(/(?<ref>\/.*) (?<qry>\/.*)/)
           if match
@@ -38,6 +39,10 @@ class OptParser
           exit(1)
         end
       end
+
+      opts.on("-s", "--sample SAMPLENAME", "gVCF Sample name") do |samplename|
+        options.samplename = samplename
+      end
     end
     opt_parser.parse!(args)
     return options
@@ -45,7 +50,6 @@ class OptParser
 end
 options = OptParser.parse(ARGV)
 
-# Open the Delta File
 d = BioMummer::DeltaFile.new(StringIO.new(`delta-filter -r -q #{options.delta}`))
 
 puts '##fileformat=VCFv4.1
@@ -57,125 +61,173 @@ puts '##fileformat=VCFv4.1
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
 ##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block">
 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">'
-
 options.ref.each do |name, seq|
   puts "##contig=<ID=#{name},length=#{seq.length}>"
 end
-puts "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tDUMMYSAMPLENAME"
+puts '##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
+##INFO=<ID=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
+##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
+##INFO=<ID=END,Number=1,Type=Integer,Description="Stop position of the interval">
+##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
+##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
+##INFO=<ID=MLEAC,Number=A,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
+##INFO=<ID=MLEAF,Number=A,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
+##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
+##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
+##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
+##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">'
+puts "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\t#{options.samplename}"
 
 d.alignments
-  .group_by{|a| a.refname}.sort_by{|refname, alignments| refname}
-  .take(2)
+  .group_by{ |alignment| alignment.refname }
+  .sort_by{ |refname, alignments| refname }
   .each do |refname, alignments|
-  cursor = 1
-  overlap = 0
-  alignments.sort_by{|a| [a.refstart, a.refstop].min}.each do |a|
-    ref = options.ref[a.refname].subseq(a.refstart, a.refstop)
-    qry = a.strand ? options.qry[a.queryname].subseq(a.querystart, a.querystop) : options.qry[a.queryname].subseq(a.querystart, a.querystop).complement
-    if a.refstart > cursor
-      puts [refname, cursor, '.', options.ref[refname][cursor].upcase, "<NON_REF>", '.', '.', "END=#{a.refstart - 1}", "GT:DP:GQ:MIN_DP:PL", "0:0:0:0:0,0"].join("\t")
-      cursor = a.refstart
-    elsif a.refstart < cursor
-      overlap = cursor - a.refstart
-    end
-    
-    a.distances.inject([0,0]) do |mem, distance|
-      if distance > 0
-        qry.insert(mem.first + distance - 1, ".")
-        [mem.first + distance, mem.last + distance]
-      else
-        ref.insert(mem.last - distance - 1, ".")
-        [mem.first - distance, mem.last - distance]
-      end
-    end
-    overlap2 = 0
-
-    ref.chars.zip(0..(ref.length-1), qry.chars).chunk do |refBase, i, qryBase|
-      if refBase == qryBase
-        "NOVAR"
-      elsif refBase == "."
-        "INS"
-      elsif qryBase == "."
-        "DEL"
+
+  clusters = Enumerator.new do |yielder|
+    # We sweep along each of the reference sequences. The cursor tracks
+    # our position as we go so we don't concatenate regions that are
+    # actually overlapping.
+    cursor = 1
+
+    # The =alignments= object is an array of BioMummer::Alignment
+    # objects that all match a particular scaffold.
+    alignments
+      .sort_by{ |alignment| alignment.refstart }.
+      each do |aln|
+      # Create Bio::Sequence::NA subsequences for the reference and
+      # query. They are initially unaligned.
+      refSeq = options.ref[aln.refname].subseq(aln.refstart, aln.refstop)
+      qrySeq = options.qry[aln.qryname].subseq(aln.qrystart, aln.qrystop)
+      qrySeq.complement! unless aln.strand
+
+      # Do we have uncovered bases before the alignment starts? These
+      # are detected as gaps between the cursor and the alignment start
+      # site in the reference.
+      gap_size = aln.refstart - cursor
+      overlap_size = 0
+      if gap_size > 0
+        # There is a stretch of reference bases without an alignment
+        gapSeq = options.ref[aln.refname].subseq(cursor, aln.refstart - 1)
+        gapSeq
+          .chars
+          .zip(("-" * gapSeq.length).chars, Range.new(cursor, aln.refstart, true))
+          .each{ |ary| yielder << ary }
+        cursor = aln.refstart
       else
-        "SNP"
-      end
-    end.drop_while do |varClass, arr|
-      if varClass != "INS"
-        overlap, overlap2 = overlap - arr.length , overlap
+        overlap_size = cursor - aln.refstart
       end
-      overlap >= 0
-    end.each do |varClass, arr|
-      case varClass
-      when "NOVAR"
-        if overlap2 > 0
-          refBase = arr[overlap2].first.upcase
+
+      # Nucmer records insertions and deletions as a series of positive
+      # and negative integers corresponding to how many steps along the
+      # alignment until you get to the next gap in the reference
+      # sequence (positive integer) or how many steps until the next gap
+      # in the query (negative integer). BioMummer exposes these as the
+      # alignments 'distances' array.
+      # We walk along the Bio::Sequence::NA objects and insert gaps
+      # (".") when needed. We store our current position in the
+      # reference and the query in a two-element array.
+      aln.distances.inject([0,0]) do |mem, distance_to_gap|
+        if distance_to_gap > 0
+          qrySeq.insert(mem[0] + distance_to_gap - 1, ".")
+          [mem[0] + distance_to_gap, mem[1] + distance_to_gap]
         else
-          refBase = arr.first.first.upcase
-          overlap2 = 0
-        end        
-        puts [refname,
-              cursor,
-              ".",
-              refBase,
-              "<NON_REF>",
-              '.',
-              '.',
-              "END=#{cursor + arr.length - 1 - overlap2};ALTSCAFF=#{a.queryname};RLEN=#{arr.length};OVERLAP2=#{overlap2}",
-              "GT:DP:GQ:MIN_DP:PL",
-              "0:200:200:200:0,800"].join("\t")
-        cursor += arr.length - overlap2
-        overlap2 = 0
-      when "SNP"
-        arr.each do |snp|
-        puts [refname,
-              cursor,
-              ".",
-              snp.first.upcase,
-              [snp.last.upcase, "<NON_REF>"].join(","),
-              '.',
-              '.',
-              "END=#{cursor};ALTSCAFF=#{a.queryname}",
-              "GT:DP:GQ:MIN_DP:PL",
-              "1:200:200:200:800,0,800"].join("\t")
-          cursor += 1
+          refSeq.insert(mem[1] - distance_to_gap - 1, ".")
+          [mem[0] - distance_to_gap, mem[1] - distance_to_gap]
         end
-        # puts [refname,
-        #       cursor,
-        #       ".",
-        #       arr.map{|a| a.first.upcase}.join,
-        #       [arr.map{|a| a.last.upcase}.join, "<NON_REF>"].join(","),
-        #       '.',
-        #       '.',
-        #       "END=#{cursor + arr.length - 1};ALTSCAFF=#{a.queryname}",
-        #       "GT:DP:GQ:MIN_DP:PL",
-        #       "1:200:200:200:800,0,800"].join("\t")
-        # cursor += arr.length
-      when "INS"
-        refBase = options.ref[refname][cursor-2].upcase
-        puts [refname,
-              cursor-1,
-              ".",
-              refBase,
-              [(refBase + arr.map{|a| a.last}.join).upcase, "<NON_REF>"].join(","),
-              '.',
-              '.',
-              "END=#{cursor - 1};ALTSCAFF=#{a.queryname};STRAND=#{a.strand}",
-              "GT:DP:GQ:MIN_DP:PL",
-              "1:200:200:200:800,0,800"].join("\t")
-      when "DEL"
-        puts [refname,
-              cursor,
-              ".",
-              arr.map{|a| a.first.upcase}.join,
-              ".,<NON_REF>",
-              '.',
-              '.',
-              "END=#{cursor + arr.length - 1};ALTSCAFF=#{a.queryname}",
-              "GT:DP:GQ:MIN_DP:PL",
-              "1:200:200:200:800,0,800"].join("\t")
-        cursor += arr.length
+      end
+
+      if overlap_size < refSeq.length
+        i = aln.refstart - 1
+        positions = refSeq.chars.map{ |base| base == '.' ? i : i+=1 }
+        refSeq
+          .chars
+          .zip(qrySeq.chars, positions)
+          .drop(overlap_size)
+          .each{ |ary| yielder << ary }
       end
     end
   end
+
+  cursor = 0
+  stolen_zipped = [nil, nil, nil]
+  chunked = clusters.find_all do |refBase, qryBase, position|
+    if position > cursor || (position == cursor && refBase == ".")
+      cursor = position
+      true
+    else
+      false
+    end
+  end.chunk do |refBase, qryBase, position|
+    # Classify runs of identiry, insertions, deletions or SNPs.
+    if refBase == qryBase 
+      :NO_VARIATION
+    elsif qryBase == "-"
+      :NO_COVERAGE
+    elsif qryBase == '.'
+      :DELETION
+    elsif refBase == '.'
+      :INSERTION
+    else
+      :SNP
+    end
+  end.to_a
+
+  chunked.each_cons(2) do |current, upcoming|
+    cur_class = current.first
+    cur_zipped = current.last
+    nxt_class = upcoming.first
+
+    if nxt_class == :INSERTION || nxt_class == :DELETION
+      stolen_zipped = cur_zipped.pop
+      next if cur_zipped.length == 0
+    end
+    
+    case cur_class
+    when :NO_COVERAGE
+      puts "#{refname}\t#{cur_zipped.first.last}\t.\t#{cur_zipped.first.first.upcase}\t<NON_REF>\t.\t.\tEND=#{cur_zipped.last.last}\tGT:DP:GQ:PL\t0:0:0:0,0"
+    when :NO_VARIATION
+      puts "#{refname}\t#{cur_zipped.first.last}\t.\t#{cur_zipped.first.first.upcase}\t<NON_REF>\t.\t.\tEND=#{cur_zipped.last.last}\tGT:DP:GQ:PL\t0:1:200:0,800"
+    when :SNP
+      cur_zipped.each do |refBase, qryBase, position|
+        puts "#{refname}\t#{position}\t.\t#{refBase.upcase}\t#{qryBase.upcase},<NON_REF>\t.\t.\tEND=#{position}\tGT:DP:GQ:PL\t1:1:200:800,0,800"
+      end
+    when :INSERTION
+      refSeq, qrySeq = cur_zipped.unshift(stolen_zipped).transpose.map{|seq| seq.reject{|c|c=='.'}.join.upcase }
+      puts "#{refname}\t#{cur_zipped.first.last}\t.\t#{refSeq}\t#{qrySeq},<NON_REF>\t.\t.\tEND=#{cur_zipped.last.last}\tGT:DP:GQ:PL\t1:1:200:800,0,800"
+    when :DELETION
+      refSeq, qrySeq = cur_zipped.unshift(stolen_zipped).transpose.map{|seq| seq.reject{|c|c=='.'}.join.upcase }
+      puts "#{refname}\t#{cur_zipped.first.last}\t.\t#{refSeq}\t#{qrySeq},<NON_REF>\t.\t.\tEND=#{cur_zipped.last.last}\tGT:DP:GQ:PL\t1:1:200:800,0,800"
+    end
+    cursor = [cursor, cur_zipped.last.last].max
+  end
+
+  # We iterated over the entries in a window of length two, outputting
+  # the first in the pair. This leaves the last entry unobserved, so
+  # we take special care to output it here
+  cur_class, cur_zipped = chunked.last
+  case cur_class
+  when :NO_COVERAGE
+    puts "#{refname}\t#{cur_zipped.first.last}\t.\t#{cur_zipped.first.first.upcase}\t<NON_REF>\t.\t.\tEND=#{cur_zipped.last.last}\tGT:DP:GQ:PL\t0:0:0:0,0"
+  when :NO_VARIATION
+    puts "#{refname}\t#{cur_zipped.first.last}\t.\t#{cur_zipped.first.first.upcase}\t<NON_REF>\t.\t.\tEND=#{cur_zipped.last.last}\tGT:DP:GQ:PL\t0:1:200:0,800"
+  when :SNP
+    cur_zipped.each do |refBase, qryBase, position|
+      puts "#{refname}\t#{position}\t.\t#{refBase.upcase}\t#{qryBase.upcase},<NON_REF>\t.\t.\tEND=#{position}\tGT:DP:GQ:PL\t1:1:200:800,0,800"
+    end
+  when :INSERTION
+    refSeq, qrySeq = cur_zipped.unshift(stolen_zipped).transpose.map{|seq| seq.reject{|c|c=='.'}.join.upcase }
+    puts "#{refname}\t#{cur_zipped.first.last}\t.\t#{refSeq}\t#{qrySeq},<NON_REF>\t.\t.\tEND=#{cur_zipped.last.last}\tGT:DP:GQ:PL\t1:1:200:800,0,800"
+  when :DELETION
+    refSeq, qrySeq = cur_zipped.unshift(stolen_zipped).transpose.map{|seq| seq.reject{|c|c=='.'}.join.upcase }
+    puts "#{refname}\t#{cur_zipped.first.last}\t.\t#{refSeq}\t#{qrySeq},<NON_REF>\t.\t.\tEND=#{cur_zipped.last.last}\tGT:DP:GQ:PL\t1:1:200:800,0,800"
+  end
+
+  # It's likely that the alignments don't run to the end of the
+  # scaffold, so we fill in to the scaffold end with the 'no coverage'
+  # entry
+  remaining = options.ref[refname].length - cursor
+  if remaining > 0
+    puts "#{refname}\t#{cursor+1}\t.\t#{options.ref[refname][cursor].upcase}\t<NON_REF>\t.\t.\tEND=#{options.ref[refname].length}\tGT:DP:GQ:PL\t0:0:0:0,0"
+  end
 end

data/lib/bio-mummer/mummer.rb

@@ -3,15 +3,15 @@ require 'stringio'
 module BioMummer
 
   class Alignment
-    attr_accessor :refname, :queryname, :refstart, :refstop, :querystart, :querystop, :strand, :distances
+    attr_accessor :refname, :qryname, :refstart, :refstop, :qrystart, :qrystop, :strand, :distances
 
-    def initialize(refname, queryname, refstart, refstop, querystart, querystop, strand, distances)
+    def initialize(refname, qryname, refstart, refstop, qrystart, qrystop, strand, distances)
       @refname = refname
-      @queryname = queryname
+      @qryname = qryname
       @refstart = refstart
       @refstop = refstop
-      @querystart = querystart
-      @querystop = querystop
+      @qrystart = qrystart
+      @qrystop = qrystop
       @strand = strand
       @distances = distances
     end
@@ -35,13 +35,13 @@ module BioMummer
 
     def ref_to_query(ref_position)
       position_in_alignment = ref_position - refstart + 1
-      querypos = nil
+      qrypos = nil
       if position_in_alignment >= deltas.length
-        querypos = @querystart - 1 + position_in_alignment + deltas.last
+        qrypos = @qrystart - 1 + position_in_alignment + deltas.last
       elsif deltas[position_in_alignment-1]
-        querypos = @querystart - 1 + position_in_alignment + deltas[position_in_alignment-1]
+        qrypos = @qrystart - 1 + position_in_alignment + deltas[position_in_alignment-1]
       end
-      !@strand && querypos ? @querystart + @querystop - querypos : querypos
+      !@strand && qrypos ? @qrystart + @qrystop - qrypos : qrypos
     end
   end
   
@@ -64,21 +64,21 @@ module BioMummer
 
     def parse(string)
       string.split("\n").slice_before(/^>/).flat_map do |block|
-        refname, queryname = block.shift.match(/>(.*) (.*) \d+ \d+/).captures
+        refname, qryname = block.shift.match(/>(.*) (.*) \d+ \d+/).captures
         block.slice_before(/\d+ \d+ \d+ \d+/).map do |alignment|
-          refstart, refstop, querystart, querystop = alignment
+          refstart, refstop, qrystart, qrystop = alignment
             .shift
             .match(/(\d+) (\d+) (\d+) (\d+) /)
             .captures
             .map{ |c| c.to_i }
           alignment.pop
           Alignment.new(refname,
-                        queryname,
+                        qryname,
                         refstart,
                         refstop,
-                        [querystart, querystop].min,
-                        [querystart, querystop].max,
-                        querystart < querystop,
+                        [qrystart, qrystop].min,
+                        [qrystart, qrystop].max,
+                        qrystart < qrystop,
                         alignment.map{ |i| i.to_i })
         end
       end
@@ -110,13 +110,13 @@ module BioMummer
         a.refname == refname && a.refstart <= startpos && a.refstop >= endpos
       end
       if a
-        queryname = a.queryname
-        querystart = a.ref_to_query(startpos)
-        querystop = a.ref_to_query(endpos)
-        if querystart.nil? || querystop.nil?
+        qryname = a.qryname
+        qrystart = a.ref_to_query(startpos)
+        qrystop = a.ref_to_query(endpos)
+        if qrystart.nil? || qrystop.nil?
           return nil
         else
-          return [queryname, querystart, querystop, a.strand]
+          return [qryname, qrystart, qrystop, a.strand]
         end
       else
         return nil

data/test/test_bio-mummer.rb

@@ -15,8 +15,8 @@ class TestBioMummer < MiniTest::Test
     assert_kind_of Fixnum, @report.alignments.first.refstart
     assert_equal 1, @report.alignments.first.refstart
     assert_equal 2435, @report.alignments.first.refstop
-    assert_equal 1, @report.alignments.first.querystart
-    assert_equal 2435, @report.alignments.first.querystop
+    assert_equal 1, @report.alignments.first.qrystart
+    assert_equal 2435, @report.alignments.first.qrystop
   end
 
   should "do basic coordinate transforms on the positive strand" do

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: bio-mummer
 version: !ruby/object:Gem::Version
-  version: 0.2.0
+  version: 0.2.1
 platform: ruby
 authors:
 - robsyme
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-03-23 00:00:00.000000000 Z
+date: 2015-03-31 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: shoulda
@@ -105,7 +105,6 @@ extra_rdoc_files:
 - README.md
 - README.rdoc
 files:
-- .document
 - .travis.yml
 - Gemfile
 - LICENSE.txt

data/.document

@@ -1,5 +0,0 @@
-lib/**/*.rb
-bin/*
-- 
-features/**/*.feature
-LICENSE.txt