bio-maf 0.2.0-java → 0.3.0-java

data/lib/bio/maf/tiler.rb

@@ -1,3 +1,4 @@
+require 'pathname'
 require 'zlib'
 
 module Bio::MAF
@@ -9,7 +10,7 @@ module Bio::MAF
 
     attr_accessor :index
     attr_accessor :parser
-    attr_accessor :reference
+    attr_reader :reference
     # GenomicInterval
     attr_accessor :interval
     attr_accessor :species
@@ -19,6 +20,25 @@ module Bio::MAF
       @species_map = {}
     end
 
+    # Set the reference sequence.
+    #
+    # @param source [FASTARangeReader, String, Pathname]
+    def reference=(source)
+      ref = case
+            when source.is_a?(FASTARangeReader)
+              source
+            when source.respond_to?(:seek)
+              # open file
+              FASTARangeReader.new(source)
+            when source.respond_to?(:start_with?) && source.start_with?('>')
+              # FASTA string
+              FASTARangeReader.new(StringIO.new(source))
+            else
+              FASTARangeReader.new(source.to_s)
+            end
+      @reference = ref
+    end
+
     def ref_data(range)
       if reference
         if reference.respond_to? :read_interval
@@ -33,8 +53,12 @@ module Bio::MAF
       end
     end
 
+    def species_to_use
+      species || species_map.keys
+    end
+
     def tile
-      parser.sequence_filter[:only_species] = @species
+      parser.sequence_filter[:only_species] = species_to_use
       # TODO: remove gaps
       blocks = index.find([interval], parser).sort_by { |b| b.vars[:score] }
       mask = Array.new(interval.length, :ref)
@@ -51,7 +75,7 @@ module Bio::MAF
                   (slice_start - i_start)...(slice_end - i_start))
       end
       text = []
-      species.each { |s| text << '' }
+      species_to_use.each { |s| text << '' }
       nonref_text = text[1...text.size]
       runs(mask) do |range, block|
         g_range = (range.begin + i_start)...(range.end + i_start)
@@ -69,7 +93,7 @@ module Bio::MAF
         else
           # covered by an alignment block
           t_range = block.ref_seq.text_range(g_range)
-          species.each_with_index do |species, i|
+          species_to_use.each_with_index do |species, i|
             sp_text = text[i]
             seq = block.sequences.find { |s| s.source == species || s.species == species }
             if seq
@@ -86,7 +110,7 @@ module Bio::MAF
     end
 
     def write_fasta(f)
-      species.zip(tile()) do |species, text|
+      species_to_use.zip(tile()) do |species, text|
         sp_out = species_map[species] || species
         f.puts ">#{sp_out}"
         f.puts text
@@ -147,10 +171,13 @@ module Bio::MAF
         line = line_raw.strip
         end_pos = pos + line.size
         if (! in_region) && pos <= z_start && z_start < end_pos
-          data << line.slice((z_start - pos)...(line.size))
+          offset = z_start - pos
+          end_offset = [(offset + region_size), line.size].min
+          data << line.slice(offset...end_offset)
           in_region = true
         elsif in_region
           need = region_size - data.size
+          raise "should not happen: region #{region_size}, data #{data.size}, need #{need}" if need < 0
           if need > line.size
             data << line
           else

data/man/maf_index.1

@@ -1,7 +1,7 @@
 .\" generated with Ronn/v0.7.3
 .\" http://github.com/rtomayko/ronn/tree/0.7.3
 .
-.TH "MAF_INDEX" "1" "June 2012" "Clayton Wheeler" "BioRuby Manual"
+.TH "MAF_INDEX" "1" "July 2012" "BioRuby" "BioRuby Manual"
 .
 .SH "NAME"
 \fBmaf_index\fR \- build and examine MAF indexes

data/man/maf_tile.1

@@ -1,22 +1,22 @@
 .\" generated with Ronn/v0.7.3
 .\" http://github.com/rtomayko/ronn/tree/0.7.3
 .
-.TH "MAF_TILE" "1" "June 2012" "Clayton Wheeler" "BioRuby Manual"
+.TH "MAF_TILE" "1" "July 2012" "BioRuby" "BioRuby Manual"
 .
 .SH "NAME"
 \fBmaf_tile\fR \- synthesize an alignment for a given region
 .
 .SH "SYNOPSIS"
-\fBmaf_tile\fR [\fIoptions\fR] \-i BEGIN:END [\-s SPECIES[:NAME] \.\.\.] \fImaf\fR \fIindex\fR
+\fBmaf_tile\fR [\fIoptions\fR] \-i [SEQ:]BEGIN:END [\-s SPECIES[:NAME] \.\.\.] \fImaf\fR [index]
 .
 .P
-\fBmaf_tile\fR [\fIoptions\fR] \-\-bed BED \-o BASE [\-s SPECIES[:NAME] \.\.\.] \fImaf\fR \fIindex\fR
+\fBmaf_tile\fR [\fIoptions\fR] \-\-bed BED \-o BASE [\-s SPECIES[:NAME] \.\.\.] \fImaf\fR [index]
 .
 .SH "DESCRIPTION"
-\fBmaf_tile\fR takes a MAF file with index (generated by maf_index(1)), extracts alignment blocks overlapping the given genomic interval, and constructs a single alignment block covering the entire interval for the specified species\. Optionally, any gaps in coverage of the MAF file\'s reference sequence can be filled in from a FASTA sequence file\.
+\fBmaf_tile\fR takes a MAF file, with optional index, or directory of indexed MAF files, extracts alignment blocks overlapping the given genomic interval, and constructs a single alignment block covering the entire interval for the specified species\. Optionally, any gaps in coverage of the MAF file\'s reference sequence can be filled in from a FASTA sequence file\.
 .
 .P
-If a single interval is specified, the output will be written to stdout in FASTA format\. If the \fB\-\-output\-base\fR option is specified, \fB_<start>:<end>\.fa\fR will be appended to the given  parameter and used to construct the output path\. If a BED file is specified with \fB\-\-bed\fR, \fB\-\-output\-base\fR is also required\.
+If a single interval is specified, the output will be written to stdout in FASTA format\. If a directory of MAF files is supplied as the \fImaf\fR parameter, the interval must include the sequence identifier in the form \fBsequence:begin:end\fR\. If the \fB\-\-output\-base\fR option is specified, \fB_<begin>:<end>\.fa\fR will be appended to the given  parameter and used to construct the output path\. If a BED file is specified with \fB\-\-bed\fR, \fB\-\-output\-base\fR is also required\.
 .
 .P
 Species can be renamed for output by specifying them as SPECIES:NAME; the first component will be used to select the species from the MAF file, and the second will be used in the FASTA description line for output\.
@@ -84,10 +84,10 @@ $ maf_tile \-\-bed /tmp/mm8\.bed \-\-output\-base /tmp/mm8 \e
 The output is generated in FASTA format, with one sequence per species\.
 .
 .P
-The input \fImaf\fR file must be a Multiple Alignment Format file\.
+The \fImaf\fR parameter must specify either a Multiple Alignment Format (MAF) file or a directory of such files, with indexes\.
 .
 .P
-The \fIindex\fR must be a MAF index built with maf_index(1)\.
+The \fIindex\fR must be a MAF index built with maf_index(1)\. This parameter is ignored if the \fImaf\fR parameter is a directory\. It can be omitted if a single MAF file is given, but in this case the entire file will be parsed to build a temporary index\. For large files which will be reused, this is not advisable\.
 .
 .P
 If \fB\-\-bed\fR \fIbed\fR is specified, its argument must be a BED file\. Only the second and third columns will be used, to specify the zero\-based start and end positions of intervals\.

data/man/maf_tile.1.ronn

@@ -3,23 +3,26 @@ maf_tile(1) -- synthesize an alignment for a given region
 
 ## SYNOPSIS
 
-`maf_tile` [<options>] -i BEGIN:END [-s SPECIES[:NAME] ...] <maf> <index>
+`maf_tile` [<options>] -i [SEQ:]BEGIN:END [-s SPECIES[:NAME] ...] <maf> [index]
 
-`maf_tile` [<options>] --bed BED -o BASE [-s SPECIES[:NAME] ...] <maf> <index>
+`maf_tile` [<options>] --bed BED -o BASE [-s SPECIES[:NAME] ...] <maf> [index]
 
 ## DESCRIPTION
 
-**maf_tile** takes a MAF file with index (generated by maf_index(1)),
-extracts alignment blocks overlapping the given genomic interval, and
-constructs a single alignment block covering the entire interval for
-the specified species. Optionally, any gaps in coverage of the MAF
-file's reference sequence can be filled in from a FASTA sequence file.
+**maf_tile** takes a MAF file, with optional index, or directory of
+indexed MAF files, extracts alignment blocks overlapping the given
+genomic interval, and constructs a single alignment block covering the
+entire interval for the specified species. Optionally, any gaps in
+coverage of the MAF file's reference sequence can be filled in from a
+FASTA sequence file.
 
 If a single interval is specified, the output will be written to
-stdout in FASTA format. If the `--output-base` option is specified,
-`_<start>:<end>.fa` will be appended to the given <base> parameter and
-used to construct the output path. If a BED file is specified with
-`--bed`, `--output-base` is also required.
+stdout in FASTA format. If a directory of MAF files is supplied as the
+<maf> parameter, the interval must include the sequence identifier in
+the form `sequence:begin:end`. If the `--output-base` option is
+specified, `_<begin>:<end>.fa` will be appended to the given <base>
+parameter and used to construct the output path. If a BED file is
+specified with `--bed`, `--output-base` is also required.
 
 Species can be renamed for output by specifying them as SPECIES:NAME;
 the first component will be used to select the species from the MAF
@@ -80,9 +83,14 @@ sequence:
 The output is generated in FASTA format, with one sequence per
 species.
 
-The input <maf> file must be a Multiple Alignment Format file.
+The <maf> parameter must specify either a Multiple Alignment Format
+(MAF) file or a directory of such files, with indexes.
 
-The <index> must be a MAF index built with maf_index(1).
+The <index> must be a MAF index built with maf_index(1). This
+parameter is ignored if the <maf> parameter is a directory. It can be
+omitted if a single MAF file is given, but in this case the entire
+file will be parsed to build a temporary index. For large files which
+will be reused, this is not advisable.
 
 If `--bed` <bed> is specified, its argument must be a BED file. Only
 the second and third columns will be used, to specify the zero-based

data/man/maf_to_fasta.1

@@ -1,7 +1,7 @@
 .\" generated with Ronn/v0.7.3
 .\" http://github.com/rtomayko/ronn/tree/0.7.3
 .
-.TH "MAF_TO_FASTA" "1" "June 2012" "Clayton Wheeler" "BioRuby Manual"
+.TH "MAF_TO_FASTA" "1" "July 2012" "BioRuby" "BioRuby Manual"
 .
 .SH "NAME"
 \fBmaf_to_fasta\fR \- convert MAF file to FASTA

data/spec/bio/maf/index_spec.rb

@@ -3,6 +3,73 @@ require 'spec_helper'
 module Bio
   module MAF
 
+    describe Access do
+      describe "#tile" do
+        it "gives correct output with a Pathname" do
+          access = Access.maf_dir(TestData)
+          interval = GenomicInterval.zero_based('sp1.chr1', 0, 50)
+          buf = StringIO.new
+          access.tile(interval) do |tiler|
+            tiler.reference = TestData + 'gap-sp1.fa'
+            tiler.species = %w(sp1 sp2 sp3)
+            tiler.write_fasta(buf)
+          end
+          buf.string.should == File.read(TestData + 'gap-filled1.fa')
+        end
+        it "gives correct output with only a species map" do
+          access = Access.maf_dir(TestData)
+          interval = GenomicInterval.zero_based('sp1.chr1', 0, 50)
+          buf = StringIO.new
+          access.tile(interval) do |tiler|
+            tiler.reference = TestData + 'gap-sp1.fa'
+            tiler.species_map = {
+              'sp1' => 'sp1',
+              'sp2' => 'sp2',
+              'sp3' => 'sp3'
+            }
+            tiler.write_fasta(buf)
+          end
+          buf.string.should == File.read(TestData + 'gap-filled1.fa')
+        end
+        it "gives correct output with no species specified" do
+          pending("issue 88") do
+            access = Access.maf_dir(TestData)
+            interval = GenomicInterval.zero_based('sp1.chr1', 0, 50)
+            buf = StringIO.new
+            access.tile(interval) do |tiler|
+              tiler.reference = TestData + 'gap-sp1.fa'
+              tiler.write_fasta(buf)
+            end
+            buf.string.should == File.read(TestData + 'gap-filled1.fa')
+          end
+        end
+      end
+      describe ".file" do
+        it "accepts a MAF file and index" do
+          access = Access.file(TestData + 'gap-1.maf',
+                               TestData + 'gap-1.kct')
+          blocks = access.find([GenomicInterval.zero_based('sp1.chr1',
+                                                           10,
+                                                           23)]).to_a
+          blocks.size.should == 1
+        end
+        it "accepts a MAF file and finds the index" do
+          access = Access.file(TestData + 'gap-1.maf')
+          blocks = access.find([GenomicInterval.zero_based('sp1.chr1',
+                                                           10,
+                                                           23)]).to_a
+          blocks.size.should == 1
+        end
+        it "accepts a MAF file and builds a temp index" do
+          access = Access.file(TestData + 'chrY-1block.maf')
+          blocks = access.find([GenomicInterval.zero_based('hg19.chrY',
+                                                           10501,
+                                                           10544)]).to_a
+          blocks.size.should == 1
+        end
+      end
+    end
+
     describe KyotoIndex do
       def has_at_least_n_with_prefix(n, start)
         @idx.db.cursor_process do |cur|
@@ -87,6 +154,38 @@ module Bio
             l[0].offset.should == 16
           end
 
+          it "takes a block arg" do
+            called = false
+            @idx.find([GenomicInterval.zero_based('mm8.chr7',
+                                                  80082334,
+                                                  80082338)],
+                      @p) do |block|
+              block.offset.should == 16
+              called = true
+            end
+            called.should be_true
+          end
+
+          it "with a block and no match, returns" do
+            called = false
+            @idx.find([GenomicInterval.zero_based('mm8.chr7',
+                                                  20082334,
+                                                  20082338)],
+                      @p) do |block|
+              called = true
+            end
+            called.should be_false
+          end
+
+          it "with no block and no match, returns an empty list" do
+            v = @idx.find([GenomicInterval.zero_based('mm8.chr7',
+                                                  20082334,
+                                                  20082338)],
+                          @p)
+            v.should_not be_nil
+            v.should respond_to(:count)
+          end
+
           after(:each) do
             @idx.db.close
             @p.f.close

data/spec/bio/maf/maf_spec.rb

@@ -0,0 +1,184 @@
+require 'spec_helper'
+
+module Bio
+  module MAF
+
+    describe Header do
+      before(:each) do
+        @p = Parser.new(TestData + 't1.maf')
+      end
+
+      it "provides version information" do
+        @p.header.version.should == '1'
+      end
+      it "provides the scoring scheme" do
+        @p.header.scoring.should == 'humor.v4'
+      end
+      it "provides alignment parameters" do
+        @p.header.alignment_params.should =~ /humor.v4 R=30/
+      end
+
+      it "presents multiline parameters correctly" do
+        @p.header.alignment_params.should == "humor.v4 R=30 M=10 /cluster/data/hg15/bed/blastz.mm3/axtNet300/chr1.maf /cluster/data/hg15/bed/blastz.rn3/axtNet300/chr1.maf"
+      end
+
+      it "provides arbitrary parameters"
+    end
+
+    describe Block do
+      describe "#find_gaps" do
+        it "finds a single 14-base gap" do
+          p = Parser.new(TestData + 'mm8_chr7_tiny.maf')
+          p.sequence_filter = { :only_species => %w(mm8 rn4 hg18 canFam2 loxAfr1) }
+          block = p.parse_block
+          gaps = block.find_gaps
+          gaps.size.should == 1
+          gaps[0][0].should == 34
+          gaps[0][1].should == 14
+        end
+      end
+      describe "#remove_gaps!" do
+        it "removes a single 14-base gap" do
+          p = Parser.new(TestData + 'mm8_chr7_tiny.maf')
+          p.sequence_filter = { :only_species => %w(mm8 rn4 hg18 canFam2 loxAfr1) }
+          block = p.parse_block
+          block.sequences.size.should == 5
+          block.text_size.should == 54
+          block.remove_gaps!
+          block.text_size.should == 40
+        end
+      end
+      describe "#joinable_with?" do
+        it "is false for blocks with different sequences" do
+          p = Parser.new(TestData + 'mm8_chr7_tiny.maf')
+          sp = %w(mm8 rn4 oryCun1 hg18 panTro2 rheMac2 canFam2 dasNov1 loxAfr1 echTel1)
+          p.sequence_filter = { :only_species => sp }
+          b1 = p.parse_block
+          b2 = p.parse_block
+          b1.joinable_with?(b2).should be_false
+        end
+        it "is true for blocks with same sequences" do
+          p = Parser.new(TestData + 'mm8_chr7_tiny.maf')
+          sp = %w(mm8 rn4 oryCun1 hg18 panTro2 rheMac2 canFam2 loxAfr1 echTel1)
+          p.sequence_filter = { :only_species => sp }
+          b1 = p.parse_block
+          b2 = p.parse_block
+          b1.joinable_with?(b2).should be_true
+        end
+      end
+      describe "#to_bio_alignment" do
+        it "returns a usable Bio::BioAlignment::Alignment" do
+          p = Parser.new(TestData + 'mm8_chr7_tiny.maf')
+          b = p.parse_block
+          ba = b.to_bio_alignment
+          ba.size.should == 10
+          ba.sequences[0].id.should == "mm8.chr7"
+          ba.sequences[0].seq.should =~ /^GGGCTGAGGGC--/
+        end
+      end
+    end
+
+    describe Sequence do
+      before(:each) do
+        @parser = DummyParser.new
+      end
+
+      describe "#gapped?" do
+        it "is false for sequences with no gaps" do
+          line = "s human_unc 9077 8 + 10998 ACAGTATT"
+          s = @parser.parse_seq_line(line, nil)
+          s.gapped?.should be_false
+        end
+        it "is true for sequences with gaps" do
+          line = "s human_unc 9077 8 + 10998 AC-AGTATT"
+          s = @parser.parse_seq_line(line, nil)
+          s.gapped?.should be_true
+        end
+      end
+
+      describe "#text_range" do
+        it "returns 0...text.size for a spanning interval" do
+          line = "s human_unc 9077 8 + 10998 ACAGTATT"
+          s = @parser.parse_seq_line(line, nil)
+          range = s.text_range(9077...(9077 + 8))
+          range.should == (0...(s.text.size))
+        end
+        it "returns 0...text.size for a gapped spanning interval" do
+          line = "s human_unc 9077 8 + 10998 AC--AGTATT"
+          s = @parser.parse_seq_line(line, nil)
+          range = s.text_range(9077...(9077 + 8))
+          range.should == (0...(s.text.size))
+        end
+        it "handles a leading subset" do
+          line = "s human_unc 9077 8 + 10998 ACAGTATT"
+          s = @parser.parse_seq_line(line, nil)
+          range = s.text_range(9077...(9077 + 2))
+          range.should == (0...2)
+        end
+        it "handles a trailing subset" do
+          line = "s human_unc 9077 8 + 10998 ACAGTATT"
+          s = @parser.parse_seq_line(line, nil)
+          range = s.text_range(9079...9085)
+          range.should == (2...8)
+        end
+        it "handles a gap in the middle" do
+          line = "s human_unc 9077 8 + 10998 AC--AGTATT"
+          s = @parser.parse_seq_line(line, nil)
+          range = s.text_range(9078...(9077 + 8))
+          range.should == (1...(s.text.size))
+        end
+        it "errors on a range starting before" do
+          expect {
+            line = "s human_unc 9077 8 + 10998 ACAGTATT"
+            s = @parser.parse_seq_line(line, nil)
+            range = s.text_range(9076...(9077 + 8))
+          }.to raise_error
+        end
+        it "errors on a range ending after" do
+          expect {
+            line = "s human_unc 9077 8 + 10998 ACAGTATT"
+            s = @parser.parse_seq_line(line, nil)
+            range = s.text_range(9076...(9077 + 9))
+          }.to raise_error
+        end
+      end
+
+      describe "synteny data" do
+        it "extracts basic data from i lines" do
+          p = Parser.new(TestData + 'chr22_ieq2.maf',
+                         :parse_extended => true)
+          b = p.parse_block
+          b.sequences[0].left_status_char.should be_nil
+          b.sequences[0].left_status.should be_nil
+          b.sequences[0].left_count.should be_nil
+          b.sequences[0].right_status_char.should be_nil
+          b.sequences[0].right_status.should be_nil
+          b.sequences[0].right_count.should be_nil
+          # works but let's not over-specify internal state
+          #b.sequences[1].i_data.should == %w(N 0 C 0)
+          b.sequences[1].left_status_char.should == 'N'
+          b.sequences[1].left_status.should == :first
+          b.sequences[1].right_status_char.should == 'C'
+          b.sequences[1].right_status.should == :contiguous
+          b.sequences[2].left_status.should == :contiguous
+          b.sequences[2].right_status_char.should == 'I'
+          b.sequences[2].right_status.should == :intervening
+          b.sequences[2].right_count.should == 146
+        end
+      end
+
+      describe "#to_bioalignment" do
+        it "returns a usable Bio::BioAlignment::Sequence" do
+          @parser = DummyParser.new
+          line = "s human_unc 9077 8 + 10998 ACAGTATT"
+          s = @parser.parse_seq_line(line, nil)
+          as = s.to_bio_alignment
+          as.id.should == "human_unc"
+          as.seq.should == "ACAGTATT"
+        end
+      end
+
+    end
+
+  end
+end