dna 0.0.7 → 0.0.8

data/lib/parsers/fasta.rb

@@ -0,0 +1,20 @@
+class FastaParser
+  
+  def initialize(handle)
+    @handle = handle
+  end
+
+  def each
+    sequence, header = nil, nil
+    @handle.each do |line|
+      if line[0].chr == '>'
+        yield Fasta.new(:name => header, :sequence => sequence) if sequence
+        sequence = ''
+        header = line[1..-1].strip
+      else
+        sequence << line.strip.tr(' ','')
+      end
+    end
+    yield Fasta.new(:name => header, :sequence => sequence)
+  end
+end

data/lib/parsers/fastq.rb

@@ -0,0 +1,26 @@
+class FastqParser
+
+  def initialize(handle)
+    @handle = handle
+  end
+  
+  def each
+    c = (0..3).cycle
+    params = { :name => nil, :sequence => nil, :quality => nil }
+    @handle.each do |line|
+      n = c.next
+      case n
+      when 0
+        params[:name] = line.strip[1..-1]
+      when 1
+        params[:sequence] = line.strip
+      when 2
+        nil
+      when 3
+        params[:quality] = line.strip
+        record = Fastq.new params
+        yield record
+      end
+    end
+  end
+end

data/lib/parsers/qseq.rb

@@ -0,0 +1,26 @@
+class QSEQParser
+
+  def initialize(handle)
+    @handle = handle
+  end
+
+  def each
+    @handle.each do |line|
+      line = line.strip.split("\t")
+      record = QSEQ.new(
+        :machine => line[0],
+        :run => line[1],
+        :lane => line[2],
+        :tile => line[3],
+        :x => line[4],
+        :y => line[5],
+        :index => line[6],
+        :read_no => line[7],
+        :sequence => line[8],
+        :quality => line[9],
+        :filtered => line[10]
+      )
+      yield record
+    end
+  end
+end

data/spec/data/test.fasta

@@ -0,0 +1,12 @@
+>1
+GAGAGATCTCAT
+GAC
+AC
+AG
+C
+CGAAG
+>2
+GAGACAUAUC
+
+CNNNA
+A

data/spec/data/test.fastq

@@ -0,0 +1,8 @@
+@1
+TGAAACTTATTGATCACCCCGCTTGGCGTTGGGGAGAAATTCAGAAAAGAGTGCTTGATGGGGCGCCACATGCCGTGCAACCCACTCTCTTTCACGCAGCGCGCCCCA
++
+5888.6778888650/-//&,(,./*-11'//0&,-0.(.,,,,/2/&-,,,,,.(.,(,..&---&-,,,((*-----*+.&,,,,,(//&,,,-(,,+(,,,--&(
+@2
+GTCGCGGCTTACCACCCAACGATTTTTTTTAGAGGTGCTGGTTTCA
++
+2550//*-1./4.--/'+.2.,,,,,,,,&(/00.11426554+13

data/spec/data/test.qseq

@@ -0,0 +1,2 @@
+HWUSI-EAS1690	0007	1	1	1139	20892	0	1	GTGTGCCAGCCGCCGCGGTAATACGTAGGTGGCAAGCGTTGTCCGGATTTATTGGGTGTAAAGGGCGCGTAGGCGGCCCTGTAAGTCAGTGGTGAAATCTC	fffffffffffffffeeeeedddddabdd\dddabeeeee^aabdcabddaKdddc`RcY`_c`aT`Ib]Tc^\cZEKOZ_\]\bZVK^UZG]`[^BBBBB	1
+HWUSI-EAS1690	0007	1	1	1174	18551	0	1	GTGTGCCAGCAGCCGCGGTAATACAGAGGGGGCAAGCGTTGTTCGGAATTACTGGGCGTAAAGGGCGCGTAGGCGGCCCGCTAAGCCGAACGTGAAATCCC	ffffffffffcffffffeffddddYdb^ddbJ]Y^eeede^eadeedLeed\ddddIdddd`ddd^edcTacaa`aJ^aLZ^]Y^BBBBBBBBBBBBBBBB	1

metadata

@@ -1,13 +1,13 @@
 --- !ruby/object:Gem::Specification 
 name: dna
 version: !ruby/object:Gem::Version 
-  hash: 17
+  hash: 15
   prerelease: 
   segments: 
   - 0
   - 0
-  - 7
-  version: 0.0.7
+  - 8
+  version: 0.0.8
 platform: ruby
 authors: 
 - Austin G. Davis-Richardson
@@ -28,9 +28,15 @@ extra_rdoc_files: []
 
 files: 
 - lib/dna.rb
+- lib/parsers/fasta.rb
+- lib/parsers/fastq.rb
+- lib/parsers/qseq.rb
 - spec/dna_spec.rb
 - spec/record_spec.rb
 - spec/spec_helper.rb
+- spec/data/test.fasta
+- spec/data/test.fastq
+- spec/data/test.qseq
 - readme.md
 homepage: http://github.com/audy/dna
 licenses: []