From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Mon, 22 Aug 2011 20:12:22 +0000 (+0000)
Subject: worked on sam.rb
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=94a4251e75ccf8a5c697654d58922c47bde10520;p=biopieces.git

worked on sam.rb

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1489 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/code_ruby/lib/maasha/sam.rb b/code_ruby/lib/maasha/sam.rb
index b45f039..4a6670d 100644
--- a/code_ruby/lib/maasha/sam.rb
+++ b/code_ruby/lib/maasha/sam.rb
@@ -32,21 +32,25 @@ class SamError < StandardError; end
 REGEX_HEADER  = Regexp.new(/^@[A-Za-z][A-Za-z](\t[A-Za-z][A-Za-z0-9]:[ -~]+)+$/)
 REGEX_COMMENT = Regexp.new(/^@CO\t.*/)
 
+# Class to parse and write SAM files.
 class Sam < Filesys
   attr_accessor :io
 
+  # Method to initialize a Sam object.
   def initialize(io = nil)
     @io          = io
     @header_hash = {}
   end
 
-  # Each header line should match: /^@[A-Za-z][A-Za-z](\t[A-Za-z][A-Za-z0-9]:[ -~]+)+$/ or /^@CO\t.*/.
+  # Method to parse the header of a SAM file.
+  # Each header line should match:
+  # /^@[A-Za-z][A-Za-z](\t[A-Za-z][A-Za-z0-9]:[ -~]+)+$/ or /^@CO\t.*/.
   # Tags containing lowercase letters are reserved for end users.
   def header
     @io.each_line do |line|
-      line.chomp!
-
       if line =~ /^@([A-Za-z][A-Za-z])/
+        line.chomp!
+
         tag = $1
 
         case tag
@@ -67,8 +71,19 @@ class Sam < Filesys
     return @header_hash.empty? ? nil : @header_hash
   end
 
+  def each
+    @io.each_line do |line|
+      unless line[0] == '@'
+        entry = parse_alignment(line.chomp)
+
+        yield entry if block_given?
+      end
+    end
+  end
+
   private
 
+  # Method to subparse header lines.
   def parse_header(line)
     hash   = {}
     fields = line.split("\t")
@@ -90,6 +105,7 @@ class Sam < Filesys
     @header_hash[:HD] = hash
   end
 
+  # Method to subparse sequence lines.
   def parse_sequence(line)
     @header_hash[:SQ] = Hash.new unless @header_hash[:SQ].is_a? Hash
     hash = {}
@@ -125,6 +141,7 @@ class Sam < Filesys
     end
   end
 
+  # Method to subparse read group lines.
   def parse_read_group(line)
     @header_hash[:RG] = Hash.new unless @header_hash[:RG].is_a? Hash
     hash = {}
@@ -166,6 +183,7 @@ class Sam < Filesys
     end
   end
 
+  # Method to subparse program lines.
   def parse_program(line)
     @header_hash[:PG] = Hash.new unless @header_hash[:PG].is_a? Hash
     hash = {}
@@ -195,6 +213,7 @@ class Sam < Filesys
     end
   end
 
+  # Method to subparse comment lines.
   def parse_comment(line)
     @header_hash[:CO] = Array.new unless @header_hash[:CO].is_a? Array
 
@@ -205,7 +224,50 @@ class Sam < Filesys
     end
   end
 
-  def get_entry
+  # Method to subparse alignment lines.
+  def parse_alignment(line)
+    fields = line.split("\t")
+
+    raise SamError, "Bad number of fields: #{fields.size} < 11" if fields.size < 11
+
+    qname = fields[0]
+    flag  = fields[1].to_i
+    rname = fields[2]
+    pos   = fields[3].to_i
+    mapq  = fields[4].to_i
+    cigar = fields[5]
+    rnext = fields[6]
+    pnext = fields[7].to_i
+    tlen  = fields[8].to_i
+    seq   = fields[9]
+    qual  = fields[10]
+
+    raise SamError, "Bad qname: #{qname}" unless qname =~ /^[!-?A-~]{1,255}$/
+    raise SamError, "Bad flag: #{flag}"   unless (0 .. 2**16 - 1).include? flag
+    raise SamError, "Bad rname: #{rname}" unless rname =~ /^(\*|[!-()+-<>-~][!-~]*)$/
+    raise SamError, "Bad pos: #{pos}"     unless (0 .. 2**29 - 1).include? pos
+    raise SamError, "Bad mapq: #{mapq}"   unless (0 .. 2**8 - 1).include? mapq
+    raise SamError, "Bad cigar: #{cigar}" unless cigar =~ /^(\*|([0-9]+[MIDNSHPX=])+)$/
+    raise SamError, "Bad rnext: #{rnext}" unless rnext =~ /^(\*|=|[!-()+-<>-~][!-~]*)$/
+    raise SamError, "Bad pnext: #{pnext}" unless (0 .. 2**29 - 1).include? pnext
+    raise SamError, "Bad tlen: #{tlen}"   unless (-2**29 + 1 .. 2**29 - 1).include? tlen
+    raise SamError, "Bad seq: #{seq}"     unless seq  =~ /^(\*|[A-Za-z=.]+)$/
+    raise SamError, "Bad qual: #{qual}"   unless qual =~ /^[!-~]+$/
+
+    entry = {}
+    entry[:QNAME] = qname
+    entry[:FLAG]  = flag
+    entry[:RNAME] = rname
+    entry[:POS]   = pos
+    entry[:MAPQ]  = mapq
+    entry[:CIGAR] = cigar
+    entry[:RNEXT] = rnext
+    entry[:PNEXT] = pnext
+    entry[:TLEN]  = tlen
+    entry[:SEQ]   = seq
+    entry[:QUAL]  = qual
+
+    entry
   end
 end
 
diff --git a/code_ruby/test/maasha/test_sam.rb b/code_ruby/test/maasha/test_sam.rb
index dc384cb..ee3c346 100755
--- a/code_ruby/test/maasha/test_sam.rb
+++ b/code_ruby/test/maasha/test_sam.rb
@@ -184,5 +184,26 @@ class SamTest < Test::Unit::TestCase
     sam = Sam.new(StringIO.new("@CO\tfubar"))
     assert_nothing_raised { sam.header }
   end
+
+  def test_Sam_each_with_bad_field_count_raises
+    fields = []
+
+    (0 ... 11).each do |i|
+      sam = Sam.new(StringIO.new(fields.join("\t") + $/))
+      assert_raise(SamError) { sam.each }
+      fields << "*"
+    end
+  end
+
+  def test_Sam_each_with_ok_field_count_dont_raise
+    sam = Sam.new(SAM_TEST)
+    assert_nothing_raised { sam.each }
+  end
+
+#  def test_Sam_each_with_bad_qname_raises
+#  end
+
+#  def test_Sam_each_with_ok_qname_dont_raise
+#  end
 end